Research Computing Center Wiki - User contributions [en]

BLAST+-Sapelo2

2022-04-08T18:00:05Z

Keeko: /* Documentation */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===

2.2.31, 2.9.0,2.10.1,2.11.0,2.12.0

=== Author / Distributor ===

[http://www.ncbi.nlm.nih.gov/ NCBI]

=== Description ===

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. More information: http://blast.ncbi.nlm.nih.gov/

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo please see the [[Lmod]] page.
To find all versions of BLAST+ installed on Sapelo2, please use module spider command to do a search, as shown below:
<pre class="gscript">
module spider BLAST+
</pre>

NCBI databases are available at Sapelo2, please refer to [[Bioinformatics_Databases]] for more details. Datasets are located in the commonly shared "/db" filesystem. [[BLAST Databases-Sapelo2 | NCBI BLAST datasets]] are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.

To use BLAST+ version 2.12.0, please first load the module, for example:
<pre class="gscript">
module load BLAST+/2.12.0-gompi-2020b
</pre>

Example of a shell script sub.sh to run blastn on the batch partition:
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_BLAST+
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST+/2.12.0-gompi-2020b
ml ncbiblastdb/20220404
blastn [options]
</pre>

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.

Submit the job to the queue with
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Running BLAST+ with multiple threads ===
Some BLAST+ commands, such as blastn, have the option to use multiple threads with the -num_threads option. Each thread should be run on one core, so the number of cpus you should request should be equal to -num_threads + 1. This accounts for the number of worker threads plus one main process thread.

To request cores, use the slurm header #SBATCH --cpus-per-task.

Below is an example, with -num_threads 8<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_BLAST+_multithread
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=9
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST+/2.12.0-gompi-2020b
ml ncbiblastdb/20220404
blastn -num_threads 8 -query example.fasta -out results.out -db nt
</pre>
=== Documentation ===
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.12.0-gompi-2020b
blastn -help
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
[-negative_taxidlist filename] [-entrez_query entrez_query]
[-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
[-subject subject_input_file] [-subject_loc range] [-query input_file]
[-out output_file] [-evalue evalue] [-word_size int_value]
[-gapopen open_penalty] [-gapextend extend_penalty]
[-perc_identity float_value] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-subject_besthit]
[-window_size int_value] [-off_diagonal_range int_value]
[-use_index boolean] [-index_name string] [-lcase_masking]
[-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format]
[-show_gis] [-num_descriptions int_value] [-num_alignments int_value]
[-line_length line_length] [-html] [-sorthits sort_hits]
[-sorthsps sort_hsps] [-max_target_seqs num_sequences]
[-num_threads int_value] [-mt_mode int_value] [-remote] [-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.12.0+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)
-strand <String, `both', `minus', `plus'>
Query strand(s) to search against database/subject
Default = `both'

*** General search options
-task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast'
'megablast' 'rmblastn' >
Task to execute
Default = `megablast'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=4>
Word size for wordfinder algorithm (length of best perfect match)
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-penalty <Integer, <=0>
Penalty for a nucleotide mismatch
-reward <Integer, >=0>
Reward for a nucleotide match
-use_index <Boolean>
Use MegaBLAST database index
Default = `false'
-index_name <String>
MegaBLAST database index name (deprecated; use only for old style indices)

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, taxids, taxidlist, negative_taxids, negative_taxidlist,
db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, taxids, taxidlist, negative_taxids, negative_taxidlist,
db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
17 = Sequence Alignment/Map (SAM),
18 = Organism Report

Options 6, 7, 10 and 17 can be additionally configured to produce
a custom format specified by space delimited format specifiers,
or in the case of options 6, 7, and 10, by a token specified
by the delim keyword. E.g.: "17 delim=@ qacc sacc score".
The delim keyword must appear after the numeric output format
specification.
The supported format specifiers for options 6, 7 and 10 are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
The supported format specifier for option 17 is:
SQ means Include Sequence Data
SR means Subject as Reference Seq
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?
-sorthits <Integer, (>=0 and =<4)>
Sorting option for hits:
alignment view options:
0 = Sort by evalue,
1 = Sort by bit score,
2 = Sort by total score,
3 = Sort by percent identity,
4 = Sort by query coverage
Not applicable for outfmt > 4
-sorthsps <Integer, (>=0 and =<4)>
Sorting option for hps:
0 = Sort by hsp evalue,
1 = Sort by hsp score,
2 = Sort by hsp query start,
3 = Sort by hsp percent identity,
4 = Sort by hsp subject start
Not applicable for outfmt != 0

*** Query filtering options
-dust <String>
Filter query sequence with DUST (Format: 'yes', 'level window linker', or
'no' to disable)
Default = `20 64 1'
-filtering_db <String>
BLAST database containing filtering elements (i.e.: repeats)
-window_masker_taxid <Integer>
Enable WindowMasker filtering using a Taxonomic ID
-window_masker_db <String>
Enable WindowMasker filtering using this repeats database.
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `true'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GIs
* Incompatible with: seqidlist, taxids, taxidlist, negative_gilist,
negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
subject_loc
-seqidlist <String>
Restrict search of database to list of SeqIDs
* Incompatible with: gilist, taxids, taxidlist, negative_gilist,
negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
subject_loc
-negative_gilist <String>
Restrict search of database to everything except the specified GIs
* Incompatible with: gilist, seqidlist, taxids, taxidlist,
negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the specified SeqIDs
* Incompatible with: gilist, seqidlist, taxids, taxidlist,
negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
subject_loc
-taxids <String>
Restrict search of database to include only the specified taxonomy IDs
(multiple IDs delimited by ',')
* Incompatible with: gilist, seqidlist, taxidlist, negative_gilist,
negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
subject_loc
-negative_taxids <String>
Restrict search of database to everything except the specified taxonomy IDs
(multiple IDs delimited by ',')
* Incompatible with: gilist, seqidlist, taxids, taxidlist,
negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
subject_loc
-taxidlist <String>
Restrict search of database to include only the specified taxonomy IDs
* Incompatible with: gilist, seqidlist, taxids, negative_gilist,
negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
subject_loc
-negative_taxidlist <String>
Restrict search of database to everything except the specified taxonomy IDs
* Incompatible with: gilist, seqidlist, taxids, taxidlist,
negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-perc_identity <Real, 0..100>
Percent identity
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-subject_besthit
Turn on best hit per subject sequence
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
(value of 5 or more is recommended)
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Discontiguous MegaBLAST options
-template_type <String, `coding', `coding_and_optimal', `optimal'>
Discontiguous MegaBLAST template type
* Requires: template_length
-template_length <Integer, Permissible values: '16' '18' '21' >
Discontiguous MegaBLAST template length
* Requires: template_type

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-no_greedy
Use non-greedy dynamic programming extension
-min_raw_gapped_score <Integer>
Minimum raw gapped score to keep an alignment in the preliminary gapped and
traceback stages
-ungapped
Perform ungapped alignment only?
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-off_diagonal_range <Integer, >=0>
Number of off-diagonals to search for the 2nd hit, use 0 to turn off
Default = `0'

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, >=1>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-mt_mode <Integer, (>=0 and =<1)>
Multi-thread mode to use in BLAST search:
0 (auto) split by database
1 split by queries
Default = `0'
* Requires: num_threads
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, taxids, taxidlist,
negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist,
subject_loc, num_threads
</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.12.0-gompi-2020b
blastp -help
USAGE
blastp [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking]
[-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-lcase_masking] [-query_loc range]
[-parse_deflines] [-outfmt format] [-show_gis]
[-num_descriptions int_value] [-num_alignments int_value]
[-line_length line_length] [-html] [-max_target_seqs num_sequences]
[-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
[-use_sw_tback] [-version]

DESCRIPTION
Protein-Protein BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)

*** General search options
-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short' >
Task to execute
Default = `blastp'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String>
Use composition-based statistics:
D or d: default (equivalent to 2 )
0 or F or f: No composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics
21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
Default = `2'

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
18 = Organism Report

Options 6, 7 and 10 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-seg <String>
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
'no' to disable)
Default = `no'
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `false'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped
Perform ungapped alignment only?

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
-use_sw_tback
Compute locally optimal Smith-Waterman alignments?

</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.12.0-gompi-2020b
blastx -help
USAGE
blastx [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-max_intron_length length] [-seg SEG_options]
[-soft_masking soft_masking] [-matrix matrix_name]
[-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-comp_based_stats compo] [-use_sw_tback] [-version]

DESCRIPTION
Translated Query-Protein Subject BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)
-strand <String, `both', `minus', `plus'>
Query strand(s) to search against database/subject
Default = `both'
-query_gencode <Integer, values between: 1-6, 9-16, 21-25>
Genetic code to use to translate query (see user manual for details)
Default = `1'

*** General search options
-task <String, Permissible values: 'blastx' 'blastx-fast' >
Task to execute
Default = `blastx'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-max_intron_length <Integer, >=0>
Length of the largest intron allowed in a translated nucleotide sequence
when linking multiple distinct alignments
Default = `0'
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String>
Use composition-based statistics:
D or d: default (equivalent to 2 )
0 or F or f: No composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics
21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
Default = `2'

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
18 = Organism Report

Options 6, 7 and 10 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-seg <String>
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
'no' to disable)
Default = `12 2.2 2.5'
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `false'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped
Perform ungapped alignment only?

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
-use_sw_tback
Compute locally optimal Smith-Waterman alignments?

</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.12.0-gompi-2020b
makeblastdb -help
USAGE
makeblastdb [-h] [-help] [-in input_file] [-input_type type]
-dbtype molecule_type [-title database_title] [-parse_seqids]
[-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
[-mask_desc mask_algo_descriptions] [-gi_mask]
[-gi_mask_name gi_based_mask_names] [-out database_name]
[-blastdb_version version] [-max_file_sz number_of_bytes]
[-logfile File_Name] [-taxid TaxID] [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
Application to create BLAST databases, version 2.12.0+

REQUIRED ARGUMENTS
-dbtype <String, `nucl', `prot'>
Molecule type of target db

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input options
-in <File_In>
Input file/database name
Default = `-'
-input_type <String, `asn1_bin', `asn1_txt', `blastdb', `fasta'>
Type of the data specified in input_file
Default = `fasta'

*** Configuration options
-title <String>
Title for BLAST database
Default = input file name provided to -in argument
-parse_seqids
Option to parse seqid for FASTA input if set, for all other input types
seqids are parsed automatically
-hash_index
Create index of sequence hash values.

*** Sequence masking options
-mask_data <String>
Comma-separated list of input files containing masking data as produced by
NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)
-mask_id <String>
Comma-separated list of strings to uniquely identify the masking algorithm
* Requires: mask_data
* Incompatible with: gi_mask
-mask_desc <String>
Comma-separated list of free form strings to describe the masking algorithm
details
* Requires: mask_id
-gi_mask
Create GI indexed masking data.
* Requires: parse_seqids
* Incompatible with: mask_id
-gi_mask_name <String>
Comma-separated list of masking data output files.
* Requires: mask_data, gi_mask

*** Output options
-out <String>
Name of BLAST database to be created
Default = input file name provided to -in argumentRequired if multiple
file(s)/database(s) are provided as input
-blastdb_version <Integer, 4..5>
Version of BLAST database to be created
Default = `5'
-max_file_sz <String>
Maximum file size for BLAST database files
Default = `1GB'
-logfile <File_Out>
File to which the program log should be redirected

*** Taxonomy options
-taxid <Integer, >=0>
Taxonomy ID to assign to all sequences
* Incompatible with: taxid_map
-taxid_map <File_In>
Text file mapping sequence IDs to taxonomy IDs.
Format:<SequenceId> <TaxonomyId><newline>
* Requires: parse_seqids
* Incompatible with: taxid

</pre>

[[#top|Back to Top]]

BLAST+-Sapelo2

2022-04-08T17:53:52Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===

2.2.31, 2.9.0,2.10.1,2.11.0,2.12.0

=== Author / Distributor ===

[http://www.ncbi.nlm.nih.gov/ NCBI]

=== Description ===

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. More information: http://blast.ncbi.nlm.nih.gov/

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo please see the [[Lmod]] page.
To find all versions of BLAST+ installed on Sapelo2, please use module spider command to do a search, as shown below:
<pre class="gscript">
module spider BLAST+
</pre>

NCBI databases are available at Sapelo2, please refer to [[Bioinformatics_Databases]] for more details. Datasets are located in the commonly shared "/db" filesystem. [[BLAST Databases-Sapelo2 | NCBI BLAST datasets]] are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.

To use BLAST+ version 2.12.0, please first load the module, for example:
<pre class="gscript">
module load BLAST+/2.12.0-gompi-2020b
</pre>

Example of a shell script sub.sh to run blastn on the batch partition:
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_BLAST+
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST+/2.12.0-gompi-2020b
ml ncbiblastdb/20220404
blastn [options]
</pre>

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.

Submit the job to the queue with
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Running BLAST+ with multiple threads ===
Some BLAST+ commands, such as blastn, have the option to use multiple threads with the -num_threads option. Each thread should be run on one core, so the number of cpus you should request should be equal to -num_threads + 1. This accounts for the number of worker threads plus one main process thread.

To request cores, use the slurm header #SBATCH --cpus-per-task.

Below is an example, with -num_threads 8<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_BLAST+_multithread
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=9
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST+/2.12.0-gompi-2020b
ml ncbiblastdb/20220404
blastn -num_threads 8 -query example.fasta -out results.out -db nt
</pre>
=== Documentation ===
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastn -help
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-perc_identity float_value]
[-qcov_hsp_perc float_value] [-max_hsps int_value]
[-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)
-strand <String, `both', `minus', `plus'>
Query strand(s) to search against database/subject
Default = `both'

*** General search options
-task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast'
'megablast' 'rmblastn' >
Task to execute
Default = `megablast'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=4>
Word size for wordfinder algorithm (length of best perfect match)
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-penalty <Integer, <=0>
Penalty for a nucleotide mismatch
-reward <Integer, >=0>
Reward for a nucleotide match
-use_index <Boolean>
Use MegaBLAST database index
Default = `false'
-index_name <String>
MegaBLAST database index name (deprecated; use only for old style indices)

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
17 = Sequence Alignment/Map (SAM),
18 = Organism Report

Options 6, 7, 10 and 17 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers for options 6, 7 and 10 are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
The supported format specifier for option 17 is:
SQ means Include Sequence Data
SR means Subject as Reference Seq
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-dust <String>
Filter query sequence with DUST (Format: 'yes', 'level window linker', or
'no' to disable)
Default = `20 64 1'
-filtering_db <String>
BLAST database containing filtering elements (i.e.: repeats)
-window_masker_taxid <Integer>
Enable WindowMasker filtering using a Taxonomic ID
-window_masker_db <String>
Enable WindowMasker filtering using this repeats database.
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `true'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-perc_identity <Real, 0..100>
Percent identity
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Discontiguous MegaBLAST options
-template_type <String, `coding', `coding_and_optimal', `optimal'>
Discontiguous MegaBLAST template type
* Requires: template_length
-template_length <Integer, Permissible values: '16' '18' '21' >
Discontiguous MegaBLAST template length
* Requires: template_type

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-no_greedy
Use non-greedy dynamic programming extension
-min_raw_gapped_score <Integer>
Minimum raw gapped score to keep an alignment in the preliminary gapped and
traceback stages
-ungapped
Perform ungapped alignment only?
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-off_diagonal_range <Integer, >=0>
Number of off-diagonals to search for the 2nd hit, use 0 to turn off
Default = `0'

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastp -help
USAGE
blastp [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking]
[-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-lcase_masking] [-query_loc range]
[-parse_deflines] [-outfmt format] [-show_gis]
[-num_descriptions int_value] [-num_alignments int_value]
[-line_length line_length] [-html] [-max_target_seqs num_sequences]
[-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
[-use_sw_tback] [-version]

DESCRIPTION
Protein-Protein BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)

*** General search options
-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short' >
Task to execute
Default = `blastp'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String>
Use composition-based statistics:
D or d: default (equivalent to 2 )
0 or F or f: No composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics
21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
Default = `2'

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
18 = Organism Report

Options 6, 7 and 10 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-seg <String>
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
'no' to disable)
Default = `no'
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `false'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped
Perform ungapped alignment only?

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
-use_sw_tback
Compute locally optimal Smith-Waterman alignments?

</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastx -help
USAGE
blastx [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-max_intron_length length] [-seg SEG_options]
[-soft_masking soft_masking] [-matrix matrix_name]
[-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-comp_based_stats compo] [-use_sw_tback] [-version]

DESCRIPTION
Translated Query-Protein Subject BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)
-strand <String, `both', `minus', `plus'>
Query strand(s) to search against database/subject
Default = `both'
-query_gencode <Integer, values between: 1-6, 9-16, 21-25>
Genetic code to use to translate query (see user manual for details)
Default = `1'

*** General search options
-task <String, Permissible values: 'blastx' 'blastx-fast' >
Task to execute
Default = `blastx'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-max_intron_length <Integer, >=0>
Length of the largest intron allowed in a translated nucleotide sequence
when linking multiple distinct alignments
Default = `0'
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String>
Use composition-based statistics:
D or d: default (equivalent to 2 )
0 or F or f: No composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics
21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
Default = `2'

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
18 = Organism Report

Options 6, 7 and 10 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-seg <String>
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
'no' to disable)
Default = `12 2.2 2.5'
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `false'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped
Perform ungapped alignment only?

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
-use_sw_tback
Compute locally optimal Smith-Waterman alignments?

</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
makeblastdb -help
USAGE
makeblastdb [-h] [-help] [-in input_file] [-input_type type]
-dbtype molecule_type [-title database_title] [-parse_seqids]
[-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
[-mask_desc mask_algo_descriptions] [-gi_mask]
[-gi_mask_name gi_based_mask_names] [-out database_name]
[-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
[-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
Application to create BLAST databases, version 2.7.1+

REQUIRED ARGUMENTS
-dbtype <String, `nucl', `prot'>
Molecule type of target db

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input options
-in <File_In>
Input file/database name
Default = `-'
-input_type <String, `asn1_bin', `asn1_txt', `blastdb', `fasta'>
Type of the data specified in input_file
Default = `fasta'

*** Configuration options
-title <String>
Title for BLAST database
Default = input file name provided to -in argument
-parse_seqids
Option to parse seqid for FASTA input if set, for all other input types
seqids are parsed automatically
-hash_index
Create index of sequence hash values.

*** Sequence masking options
-mask_data <String>
Comma-separated list of input files containing masking data as produced by
NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)
-mask_id <String>
Comma-separated list of strings to uniquely identify the masking algorithm
* Requires: mask_data
* Incompatible with: gi_mask
-mask_desc <String>
Comma-separated list of free form strings to describe the masking algorithm
details
* Requires: mask_id
-gi_mask
Create GI indexed masking data.
* Requires: parse_seqids
* Incompatible with: mask_id
-gi_mask_name <String>
Comma-separated list of masking data output files.
* Requires: mask_data, gi_mask

*** Output options
-out <String>
Name of BLAST database to be created
Default = input file name provided to -in argumentRequired if multiple
file(s)/database(s) are provided as input
-max_file_sz <String>
Maximum file size for BLAST database files
Default = `1GB'
-logfile <File_Out>
File to which the program log should be redirected

*** Taxonomy options
-taxid <Integer, >=0>
Taxonomy ID to assign to all sequences
* Incompatible with: taxid_map
-taxid_map <File_In>
Text file mapping sequence IDs to taxonomy IDs.
Format:<SequenceId> <TaxonomyId><newline>
* Requires: parse_seqids
* Incompatible with: taxid

</pre>

[[#top|Back to Top]]

BLAST+-Sapelo2

2022-04-08T17:53:38Z

Keeko:

[[Category:Sapelo2old]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===

2.2.31, 2.9.0,2.10.1,2.11.0,2.12.0

=== Author / Distributor ===

[http://www.ncbi.nlm.nih.gov/ NCBI]

=== Description ===

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. More information: http://blast.ncbi.nlm.nih.gov/

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo please see the [[Lmod]] page.
To find all versions of BLAST+ installed on Sapelo2, please use module spider command to do a search, as shown below:
<pre class="gscript">
module spider BLAST+
</pre>

NCBI databases are available at Sapelo2, please refer to [[Bioinformatics_Databases]] for more details. Datasets are located in the commonly shared "/db" filesystem. [[BLAST Databases-Sapelo2 | NCBI BLAST datasets]] are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.

To use BLAST+ version 2.12.0, please first load the module, for example:
<pre class="gscript">
module load BLAST+/2.12.0-gompi-2020b
</pre>

Example of a shell script sub.sh to run blastn on the batch partition:
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_BLAST+
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST+/2.12.0-gompi-2020b
ml ncbiblastdb/20220404
blastn [options]
</pre>

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.

Submit the job to the queue with
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Running BLAST+ with multiple threads ===
Some BLAST+ commands, such as blastn, have the option to use multiple threads with the -num_threads option. Each thread should be run on one core, so the number of cpus you should request should be equal to -num_threads + 1. This accounts for the number of worker threads plus one main process thread.

To request cores, use the slurm header #SBATCH --cpus-per-task.

Below is an example, with -num_threads 8<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_BLAST+_multithread
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=9
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST+/2.12.0-gompi-2020b
ml ncbiblastdb/20220404
blastn -num_threads 8 -query example.fasta -out results.out -db nt
</pre>
=== Documentation ===
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastn -help
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-perc_identity float_value]
[-qcov_hsp_perc float_value] [-max_hsps int_value]
[-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)
-strand <String, `both', `minus', `plus'>
Query strand(s) to search against database/subject
Default = `both'

*** General search options
-task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast'
'megablast' 'rmblastn' >
Task to execute
Default = `megablast'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=4>
Word size for wordfinder algorithm (length of best perfect match)
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-penalty <Integer, <=0>
Penalty for a nucleotide mismatch
-reward <Integer, >=0>
Reward for a nucleotide match
-use_index <Boolean>
Use MegaBLAST database index
Default = `false'
-index_name <String>
MegaBLAST database index name (deprecated; use only for old style indices)

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
17 = Sequence Alignment/Map (SAM),
18 = Organism Report

Options 6, 7, 10 and 17 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers for options 6, 7 and 10 are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
The supported format specifier for option 17 is:
SQ means Include Sequence Data
SR means Subject as Reference Seq
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-dust <String>
Filter query sequence with DUST (Format: 'yes', 'level window linker', or
'no' to disable)
Default = `20 64 1'
-filtering_db <String>
BLAST database containing filtering elements (i.e.: repeats)
-window_masker_taxid <Integer>
Enable WindowMasker filtering using a Taxonomic ID
-window_masker_db <String>
Enable WindowMasker filtering using this repeats database.
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `true'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-perc_identity <Real, 0..100>
Percent identity
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Discontiguous MegaBLAST options
-template_type <String, `coding', `coding_and_optimal', `optimal'>
Discontiguous MegaBLAST template type
* Requires: template_length
-template_length <Integer, Permissible values: '16' '18' '21' >
Discontiguous MegaBLAST template length
* Requires: template_type

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-no_greedy
Use non-greedy dynamic programming extension
-min_raw_gapped_score <Integer>
Minimum raw gapped score to keep an alignment in the preliminary gapped and
traceback stages
-ungapped
Perform ungapped alignment only?
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-off_diagonal_range <Integer, >=0>
Number of off-diagonals to search for the 2nd hit, use 0 to turn off
Default = `0'

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastp -help
USAGE
blastp [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking]
[-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-lcase_masking] [-query_loc range]
[-parse_deflines] [-outfmt format] [-show_gis]
[-num_descriptions int_value] [-num_alignments int_value]
[-line_length line_length] [-html] [-max_target_seqs num_sequences]
[-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
[-use_sw_tback] [-version]

DESCRIPTION
Protein-Protein BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)

*** General search options
-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short' >
Task to execute
Default = `blastp'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String>
Use composition-based statistics:
D or d: default (equivalent to 2 )
0 or F or f: No composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics
21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
Default = `2'

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
18 = Organism Report

Options 6, 7 and 10 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-seg <String>
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
'no' to disable)
Default = `no'
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `false'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped
Perform ungapped alignment only?

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
-use_sw_tback
Compute locally optimal Smith-Waterman alignments?

</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastx -help
USAGE
blastx [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-max_intron_length length] [-seg SEG_options]
[-soft_masking soft_masking] [-matrix matrix_name]
[-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-comp_based_stats compo] [-use_sw_tback] [-version]

DESCRIPTION
Translated Query-Protein Subject BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)
-strand <String, `both', `minus', `plus'>
Query strand(s) to search against database/subject
Default = `both'
-query_gencode <Integer, values between: 1-6, 9-16, 21-25>
Genetic code to use to translate query (see user manual for details)
Default = `1'

*** General search options
-task <String, Permissible values: 'blastx' 'blastx-fast' >
Task to execute
Default = `blastx'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-max_intron_length <Integer, >=0>
Length of the largest intron allowed in a translated nucleotide sequence
when linking multiple distinct alignments
Default = `0'
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String>
Use composition-based statistics:
D or d: default (equivalent to 2 )
0 or F or f: No composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics
21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
Default = `2'

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
18 = Organism Report

Options 6, 7 and 10 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-seg <String>
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
'no' to disable)
Default = `12 2.2 2.5'
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `false'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped
Perform ungapped alignment only?

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
-use_sw_tback
Compute locally optimal Smith-Waterman alignments?

</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
makeblastdb -help
USAGE
makeblastdb [-h] [-help] [-in input_file] [-input_type type]
-dbtype molecule_type [-title database_title] [-parse_seqids]
[-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
[-mask_desc mask_algo_descriptions] [-gi_mask]
[-gi_mask_name gi_based_mask_names] [-out database_name]
[-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
[-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
Application to create BLAST databases, version 2.7.1+

REQUIRED ARGUMENTS
-dbtype <String, `nucl', `prot'>
Molecule type of target db

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input options
-in <File_In>
Input file/database name
Default = `-'
-input_type <String, `asn1_bin', `asn1_txt', `blastdb', `fasta'>
Type of the data specified in input_file
Default = `fasta'

*** Configuration options
-title <String>
Title for BLAST database
Default = input file name provided to -in argument
-parse_seqids
Option to parse seqid for FASTA input if set, for all other input types
seqids are parsed automatically
-hash_index
Create index of sequence hash values.

*** Sequence masking options
-mask_data <String>
Comma-separated list of input files containing masking data as produced by
NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)
-mask_id <String>
Comma-separated list of strings to uniquely identify the masking algorithm
* Requires: mask_data
* Incompatible with: gi_mask
-mask_desc <String>
Comma-separated list of free form strings to describe the masking algorithm
details
* Requires: mask_id
-gi_mask
Create GI indexed masking data.
* Requires: parse_seqids
* Incompatible with: mask_id
-gi_mask_name <String>
Comma-separated list of masking data output files.
* Requires: mask_data, gi_mask

*** Output options
-out <String>
Name of BLAST database to be created
Default = input file name provided to -in argumentRequired if multiple
file(s)/database(s) are provided as input
-max_file_sz <String>
Maximum file size for BLAST database files
Default = `1GB'
-logfile <File_Out>
File to which the program log should be redirected

*** Taxonomy options
-taxid <Integer, >=0>
Taxonomy ID to assign to all sequences
* Incompatible with: taxid_map
-taxid_map <File_In>
Text file mapping sequence IDs to taxonomy IDs.
Format:<SequenceId> <TaxonomyId><newline>
* Requires: parse_seqids
* Incompatible with: taxid

</pre>

[[#top|Back to Top]]

Software

2022-04-08T17:50:57Z

Keeko: /* Partial List of Installed Software */

,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-












| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 18 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.2.31, 2.9.0, 2.10.1,2.11.0,2.12.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
































| [[cryoSPARC-Sapelo2|cryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.0, 1.1, 1.2, 1.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 4.5.6,2019.4,2020,2020.3,2021.2,2021.3,2021.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
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| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Mothur-Sapelo2|Mothur]] || 1.39.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
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| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 3.7.4, 2.7.16 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 3.5.0, 3.6.2, 4.0.0, 4.1.0 || [[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
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| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2020.28.61328, 2021.16.61629 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
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| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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| [[StringTie-Teaching|StringTie]] || 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
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| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

BLAST+-Sapelo2

2022-04-08T17:27:06Z

Keeko: Created page with "Category:Sapelo2oldCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.2.31, 2.9.0,2.10.1,..."

[[Category:Sapelo2old]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===

2.2.31, 2.9.0,2.10.1,2.11.0,2.12.0

=== Author / Distributor ===

[http://www.ncbi.nlm.nih.gov/ NCBI]

=== Description ===

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. More information: http://blast.ncbi.nlm.nih.gov/

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo please see the [[Lmod]] page.
To find all versions of BLAST+ installed on Sapelo2, please use module spider command to do a search, as shown below:
<pre class="gscript">
module spider BLAST+
</pre>

NCBI databases are available at Sapelo2, please refer to [[Bioinformatics_Databases]] for more details. Datasets are located in the commonly shared "/db" filesystem. [[BLAST Databases-Sapelo2 | NCBI BLAST datasets]] are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.

To use BLAST+ version 2.12.0, please first load the module, for example:
<pre class="gscript">
module load BLAST+/2.12.0-gompi-2020b
</pre>

Example of a shell script sub.sh to run blastn on the batch partition:
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_BLAST+
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST+/2.9.0-gompi-2019b
ml ncbiblastdb/20220404
blastn [options]
</pre>

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.

Submit the job to the queue with
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Running BLAST+ with multiple threads ===
Some BLAST+ commands, such as blastn, have the option to use multiple threads with the -num_threads option. Each thread should be run on one core, so the number of cpus you should request should be equal to -num_threads + 1. This accounts for the number of worker threads plus one main process thread.

To request cores, use the slurm header #SBATCH --cpus-per-task.

Below is an example, with -num_threads 8<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_BLAST+_multithread
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=9
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST+/2.9.0-gompi-2019b
ml ncbiblastdb/20220404
blastn -num_threads 8 -query example.fasta -out results.out -db nt
</pre>
=== Documentation ===
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastn -help
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-perc_identity float_value]
[-qcov_hsp_perc float_value] [-max_hsps int_value]
[-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)
-strand <String, `both', `minus', `plus'>
Query strand(s) to search against database/subject
Default = `both'

*** General search options
-task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast'
'megablast' 'rmblastn' >
Task to execute
Default = `megablast'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=4>
Word size for wordfinder algorithm (length of best perfect match)
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-penalty <Integer, <=0>
Penalty for a nucleotide mismatch
-reward <Integer, >=0>
Reward for a nucleotide match
-use_index <Boolean>
Use MegaBLAST database index
Default = `false'
-index_name <String>
MegaBLAST database index name (deprecated; use only for old style indices)

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
17 = Sequence Alignment/Map (SAM),
18 = Organism Report

Options 6, 7, 10 and 17 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers for options 6, 7 and 10 are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
The supported format specifier for option 17 is:
SQ means Include Sequence Data
SR means Subject as Reference Seq
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-dust <String>
Filter query sequence with DUST (Format: 'yes', 'level window linker', or
'no' to disable)
Default = `20 64 1'
-filtering_db <String>
BLAST database containing filtering elements (i.e.: repeats)
-window_masker_taxid <Integer>
Enable WindowMasker filtering using a Taxonomic ID
-window_masker_db <String>
Enable WindowMasker filtering using this repeats database.
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `true'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-perc_identity <Real, 0..100>
Percent identity
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Discontiguous MegaBLAST options
-template_type <String, `coding', `coding_and_optimal', `optimal'>
Discontiguous MegaBLAST template type
* Requires: template_length
-template_length <Integer, Permissible values: '16' '18' '21' >
Discontiguous MegaBLAST template length
* Requires: template_type

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-no_greedy
Use non-greedy dynamic programming extension
-min_raw_gapped_score <Integer>
Minimum raw gapped score to keep an alignment in the preliminary gapped and
traceback stages
-ungapped
Perform ungapped alignment only?
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-off_diagonal_range <Integer, >=0>
Number of off-diagonals to search for the 2nd hit, use 0 to turn off
Default = `0'

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastp -help
USAGE
blastp [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking]
[-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-lcase_masking] [-query_loc range]
[-parse_deflines] [-outfmt format] [-show_gis]
[-num_descriptions int_value] [-num_alignments int_value]
[-line_length line_length] [-html] [-max_target_seqs num_sequences]
[-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
[-use_sw_tback] [-version]

DESCRIPTION
Protein-Protein BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)

*** General search options
-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short' >
Task to execute
Default = `blastp'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String>
Use composition-based statistics:
D or d: default (equivalent to 2 )
0 or F or f: No composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics
21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
Default = `2'

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
18 = Organism Report

Options 6, 7 and 10 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-seg <String>
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
'no' to disable)
Default = `no'
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `false'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped
Perform ungapped alignment only?

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
-use_sw_tback
Compute locally optimal Smith-Waterman alignments?

</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastx -help
USAGE
blastx [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-max_intron_length length] [-seg SEG_options]
[-soft_masking soft_masking] [-matrix matrix_name]
[-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-comp_based_stats compo] [-use_sw_tback] [-version]

DESCRIPTION
Translated Query-Protein Subject BLAST 2.7.1+

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input query options
-query <File_In>
Input file name
Default = `-'
-query_loc <String>
Location on the query sequence in 1-based offsets (Format: start-stop)
-strand <String, `both', `minus', `plus'>
Query strand(s) to search against database/subject
Default = `both'
-query_gencode <Integer, values between: 1-6, 9-16, 21-25>
Genetic code to use to translate query (see user manual for details)
Default = `1'

*** General search options
-task <String, Permissible values: 'blastx' 'blastx-fast' >
Task to execute
Default = `blastx'
-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-out <File_Out>
Output file name
Default = `-'
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-max_intron_length <Integer, >=0>
Length of the largest intron allowed in a translated nucleotide sequence
when linking multiple distinct alignments
Default = `0'
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String>
Use composition-based statistics:
D or d: default (equivalent to 2 )
0 or F or f: No composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics
21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
Default = `2'

*** BLAST-2-Sequences options
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with: db, gilist, seqidlist, negative_gilist,
negative_seqidlist, db_soft_mask, db_hard_mask, remote

*** Formatting options
-outfmt <String>
alignment view options:
0 = Pairwise,
1 = Query-anchored showing identities,
2 = Query-anchored no identities,
3 = Flat query-anchored showing identities,
4 = Flat query-anchored no identities,
5 = BLAST XML,
6 = Tabular,
7 = Tabular with comment lines,
8 = Seqalign (Text ASN.1),
9 = Seqalign (Binary ASN.1),
10 = Comma-separated values,
11 = BLAST archive (ASN.1),
12 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
18 = Organism Report

Options 6, 7 and 10 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxid means Subject Taxonomy ID
ssciname means Subject Scientific Name
scomname means Subject Common Name
sblastname means Subject Blast Name
sskingdom means Subject Super Kingdom
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
qcovus means Query Coverage Per Unique Subject (blastn only)
When not provided, the default value is:
'qaccver saccver pident length mismatch gapopen qstart qend sstart send
evalue bitscore', which is equivalent to the keyword 'std'
Default = `0'
-show_gis
Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4
Default = `500'
* Incompatible with: max_target_seqs
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
* Incompatible with: max_target_seqs
-line_length <Integer, >=1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-html
Produce HTML output?

*** Query filtering options
-seg <String>
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
'no' to disable)
Default = `12 2.2 2.5'
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `false'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, negative_seqidlist,
remote, subject, subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, negative_seqidlist, remote,
subject, subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-negative_seqidlist <String>
Restrict search of database to everything except the listed SeqIDs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: db_hard_mask, subject, subject_loc
-db_hard_mask <String>
Filtering algorithm ID to apply to the BLAST database as hard masking
* Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100>
Percent query coverage per hsp
-max_hsps <Integer, >=1>
Set maximum number of HSPs per subject sequence to save for each query
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with: num_descriptions, num_alignments

*** Statistical options
-dbsize <Int8>
Effective length of the database
-searchsp <Int8, >=0>
Effective length of the search space
-sum_stats <Boolean>
Use sum statistics

*** Search strategy options
-import_search_strategy <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
File name to record the search strategy used
* Incompatible with: import_search_strategy

*** Extension options
-xdrop_ungap <Real>
X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real>
X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real>
X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped
Perform ungapped alignment only?

*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be parsed?
-num_threads <Integer, (>=1 and =<48)>
Number of threads (CPUs) to use in the BLAST search
Default = `1'
* Incompatible with: remote
-remote
Execute search remotely?
* Incompatible with: gilist, seqidlist, negative_gilist,
negative_seqidlist, subject_loc, num_threads
-use_sw_tback
Compute locally optimal Smith-Waterman alignments?

</pre>
[[#blastn| jump to blastn]]; [[#blastp| jump to blastp]]; [[#blastx| jump to blastx]]; [[#makeblastdb| jump to makeblastdb]]; [[#top|Back to Top]]


<pre class="gcommand">
module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
makeblastdb -help
USAGE
makeblastdb [-h] [-help] [-in input_file] [-input_type type]
-dbtype molecule_type [-title database_title] [-parse_seqids]
[-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
[-mask_desc mask_algo_descriptions] [-gi_mask]
[-gi_mask_name gi_based_mask_names] [-out database_name]
[-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
[-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
Application to create BLAST databases, version 2.7.1+

REQUIRED ARGUMENTS
-dbtype <String, `nucl', `prot'>
Molecule type of target db

OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
Print version number; ignore other arguments

*** Input options
-in <File_In>
Input file/database name
Default = `-'
-input_type <String, `asn1_bin', `asn1_txt', `blastdb', `fasta'>
Type of the data specified in input_file
Default = `fasta'

*** Configuration options
-title <String>
Title for BLAST database
Default = input file name provided to -in argument
-parse_seqids
Option to parse seqid for FASTA input if set, for all other input types
seqids are parsed automatically
-hash_index
Create index of sequence hash values.

*** Sequence masking options
-mask_data <String>
Comma-separated list of input files containing masking data as produced by
NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)
-mask_id <String>
Comma-separated list of strings to uniquely identify the masking algorithm
* Requires: mask_data
* Incompatible with: gi_mask
-mask_desc <String>
Comma-separated list of free form strings to describe the masking algorithm
details
* Requires: mask_id
-gi_mask
Create GI indexed masking data.
* Requires: parse_seqids
* Incompatible with: mask_id
-gi_mask_name <String>
Comma-separated list of masking data output files.
* Requires: mask_data, gi_mask

*** Output options
-out <String>
Name of BLAST database to be created
Default = input file name provided to -in argumentRequired if multiple
file(s)/database(s) are provided as input
-max_file_sz <String>
Maximum file size for BLAST database files
Default = `1GB'
-logfile <File_Out>
File to which the program log should be redirected

*** Taxonomy options
-taxid <Integer, >=0>
Taxonomy ID to assign to all sequences
* Incompatible with: taxid_map
-taxid_map <File_In>
Text file mapping sequence IDs to taxonomy IDs.
Format:<SequenceId> <TaxonomyId><newline>
* Requires: parse_seqids
* Incompatible with: taxid

</pre>

[[#top|Back to Top]]

Software

2022-04-08T16:21:40Z

Keeko: add BLAST+ sapelo2 row

,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-












| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 18 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.2.31, 2.9.0, 2.10.1,2.11.0,2.12.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] |[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
































| [[cryoSPARC-Sapelo2|cryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.0, 1.1, 1.2, 1.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 4.5.6,2019.4,2020,2020.3,2021.2,2021.3,2021.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Mothur-Sapelo2|Mothur]] || 1.39.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 3.7.4, 2.7.16 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 3.5.0, 3.6.2, 4.0.0, 4.1.0 || [[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2020.28.61328, 2021.16.61629 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->































| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

































| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

NCBI Fasta-Sapelo2

2022-03-08T15:19:58Z

Keeko: add new databases

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

These fasta are updated at every first business day of the month.

Each fasta is located at the directory with the name pattern /db/ncbi/fasta/month-date-year,. For example, a database downloaded on May 1, 2017 would be located at /db/ncbi/fasta/05012017

The following databases are available:

<pre class="gscript">
est_human,
est_mouse,
est_others,
est_nr,
est_nt,
nr,
nt,
htgs,
gss,
human_genomic
</pre>

Data source: [ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ NCBI Fasta FTP]

[[#top|Back to Top]]

Uniref-Sapelo2

2022-03-08T15:08:33Z

Keeko: change most recent database date

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]
latest version:
Uniref100, Uniref90, Uniref50 /db/uniref/06282018 updated at 02/25/2022 

uniref100 
uniref90 
uniref50 
<pre class="gscript">
/db/uniref/latest/uniref100
/db/uniref/latest/uniref90
/db/uniref/latest/uniref50
</pre>

The command generated the data is documented at UGA file sitting at the same directory with data:
<pre class="gcommand">
module load BLAST+/2.11.0-gompi-2020b
makeblastdb -in uniref100.fasta -dbtype prot -title uniref100 -out uniref100 -logfile uniref100.log
makeblastdb -in uniref90.fasta -dbtype prot -title uniref90 -out uniref90 -logfile uniref90.log
makeblastdb -in uniref50.fasta -dbtype prot -title uniref50 -out uniref50 -logfile uniref50.log
</pre>

Details at UniRef at the [http://www.ebi.ac.uk/uniref/ EBI] 
Data Source: [ftp://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/ UniRef] at the EBI FTP

Software

2022-03-03T02:12:10Z

Keeko: added sentence to emphasize software list is partial

,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-












| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-





| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
































| [[cryoSPARC-Sapelo2|cryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-










| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 4.5.6,2019.4,2020,2020.3,2021.2,2021.3,2021.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Mothur-Sapelo2|Mothur]] || 1.39.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 3.7.4, 2.7.16 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 3.5.0, 3.6.2, 4.0.0, 4.1.0 || [[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2020.28.61328, 2021.16.61629 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->































| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

































| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

Uniref-Sapelo2

2022-02-25T21:39:14Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]
latest version:
Uniref100, Uniref90, Uniref50 /db/uniref/06282018] updated at 06/28/2017 

uniref100 
uniref90 
uniref50 
<pre class="gscript">
/db/uniref/latest/uniref100
/db/uniref/latest/uniref90
/db/uniref/latest/uniref50
</pre>

The command generated the data is documented at UGA file sitting at the same directory with data:
<pre class="gcommand">
module load BLAST+/2.11.0-gompi-2020b
makeblastdb -in uniref100.fasta -dbtype prot -title uniref100 -out uniref100 -logfile uniref100.log
makeblastdb -in uniref90.fasta -dbtype prot -title uniref90 -out uniref90 -logfile uniref90.log
makeblastdb -in uniref50.fasta -dbtype prot -title uniref50 -out uniref50 -logfile uniref50.log
</pre>

Details at UniRef at the [http://www.ebi.ac.uk/uniref/ EBI] 
Data Source: [ftp://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/ UniRef] at the EBI FTP

Bioinformatics Databases

2022-02-25T21:36:49Z

Keeko: update latast version uniref

As part of our services, the GACRC builds and hosts local copies of frequently cited application data, and provides assistance for sharing data among GACRC members. Datasets are located in the commonly shared "/db" filesystem. [[BLAST Databases-Sapelo2 | NCBI BLAST datasets]] are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.

NCBI BLAST Datasets can be loaded in the same way as software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:

<code>ml spider ncbiblastdb</code>

You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:

<code>module load ncbiblastdb/20210616</code>

Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
module load ncbiblastdb/20210616 
blastn -query example.fasta -out results.out -db nt 
</div>

In your actual submission script, use your own discretion for the Slurm header values.

NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

Various subject datasets, e.g. pfam, bowtie indexes of human and mouse, and NCBI bacterial datasets, are hosted as well. However, these datasets are not accessed with a module. These datasets either don’t need updating, the source does not update frequently, or the datasets are not used frequently by our users. These datasets will only be updated by user request.
Instead of using a module, to use these databases, use the path to the databases in your script. Below is an example using BLAST+ with a dataset not available as a module.

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
blastn -query example.fasta -out results.out -db /db/ncbiblast/refseq_microbial/fasta/09162020/ 
</div>

For datasets requested by individual lab groups, GACRC encourages users to maintain their own copies of databases, whose files can be installed in their group's shared "/work" area.
Similarly for datasets frequently updated by their source, the GACRC encourages users to maintain their own copies of these public databases.

The set of data which are regularly updated is open to review, and can be expanded based on available GACRC resources.

==Installed Bioinformatics Databases ==
{| border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" | Name
! scope="col" class="unsortable" | Version
! scope="col" | Module Available
|-
| akblab || 01/28/2018 || no
|-
| [[Bacteria NCBI-sapelo2|Bacteria NCBI]] || 12/21/2017 || no
|-
| [[bowtie2|hg19,mm10 & mm9]] || 07/29/2016 || no
|-
| cellranger || 10/29/2019 || no
|-
| conspred_ressources || 02/02/2017 || no
|-
| dammit || 03/18/2021 || no
|-
| deconseq || 12/01/2016 || no
|-
| decontaMiner-Sapelo2|decontaMiner || 08/29/2019 || no
|-
| eggnog-mapper || 04/16/2019 || no
|-
| funannotate || 08/15/2019 || no
|-
| DTDB-Tk || 01/15/2021 || no
|-
| hg || 09/20/2016 || no
|-
| kegg || 09/09/2016 || no
|-
| maker || 05/22/2018 || no
|-
| MetaCLADE || 08/29/2019 || no
|-
| [[BLAST Databases-Sapelo2 | NCBI BLAST Databases]] || beginning of every month || yes
|-
| [[NCBI Fasta-Sapelo2|NCBI Fasta]] || beginning of every month || yes
|-
| ngs || 11/03/2016 || no
|-
| nndb || 04/29/2020 || no
|-
| PB || 04/24/2019 || no
|-
| [[PfamDB-Sapelo2|pfam]] || 10/07/2021 || no
|-
| pylosift || 07/20/2020 || no
|-
| [[Refseq-Sapelo2|Refseq_genomic]] || || no
|-
| repbase || 01/09/2017 || no
|-
| rfam || 02/09/2017 || no
|-
| seqdb || 05/23/2019 || no
|-
| sortmerna || 02/02/2021 || no
|-
| [[TaxDB-Sapelo2|TaxDB]] || 02/26/2019 || no
|-
| topcons2 || 02/18/2021 || no
|-
| [[Uniprot-Sapelo2|Uniprot]] || 11/19/2020 || no
|-
| [[Uniref-Sapelo2|Uniref]] || 02/25/2022 || no
|-
| [[wublast-Sapelo2|wublast]] || 03/01/2020 || no
|-
|}

Mothur-Sapelo2

2022-02-24T14:30:38Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
1.43.0,1.45.2,1.47.0

=== Author / Distributor ===
Please see [https://mothur.org/wiki/ Mothur]

=== Description ===
"Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. The functionality of different software including dotur, sons, treeclimber, s-libshuff, unifrac, and others have been incorperated in Mothur. In addition to improving the flexibility of these software, a number of other features including calculators and visualization tools are available with Mothur."
More details, documentation and tutorials are at the[https://mothur.org/wiki/ Mothur Wiki]

=== Running Program ===
Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

The latest version of this application is at /apps/eb/Mothur/1.47.0-GCCcore-8.3.0

To use this version, please load the module with
<pre class="gscript">
ml Mothur/1.47.0-GCCcore-8.3.0
</pre>
To run mother in "batch mode", collect your Mothur commands into a command file and use that file in a batch job. More information about creating Mothur batch files can be found here: https://mothur.org/wiki/batch_mode/
Some Mothur commands can use multiple cores. To use multiple cores, adjust the processors parameter for each command in the Mothur command file. You must also adjust the --cpus_per_task parameter in your submission script to be equal to the number of processors you request in your Mothur command file.

The following is an example of a Mothur command file requesting use of 8 cpus.This file is called Mother_Commandfile.txt, and assembles pair end reads and prepares them for analysis.

<pre class="gscript">
make.file(inputdir=./MiSeq_SOP, type=gz, prefix=stability)
make.contigs(file=current, processors=8)
screen.seqs(fasta=current, group=current, maxambig=0, maxlength=275)
unique.seqs()
count.seqs(name=current, group=current)
align.seqs(fasta=current, reference=silva.v4.fasta)
</pre>

he following is an example job submission script (sub.sh) running the above Mother command file:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=Mothurtest # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task=8 # Use 8 cpus
#SBATCH --mem=10gb # Job memory request
#SBATCH --time=02:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x_%j.out # Standard output log
#SBATCH --error=%x_%j.err # Standard error log

#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu # Where to send mail

cd $SLURM_SUBMIT_DIR
module load Mothur/1.47.0-GCCcore-8.3.0"
mothur Mother_Commandfile.txt

</pre>

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Mothur/1.47.0-GCCcore-8.3.0
mothur --help
Linux version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at https://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Script Mode

mothur > help()

NOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.

Clustering commmands include: cluster, cluster.classic, cluster.fit, cluster.split, mgcluster, phylotype

General commmands include: get.current, get.dists, make.biom, make.file, make.group, make.lefse, merge.count, merge.files, merge.groups, remove.dists, rename.file, set.current, set.dir, set.logfile, set.seed, system

Hypothesis Testing commmands include: amova, anosim, clearcut, cooccurrence, corr.axes, deunique.tree, homova, indicator, kruskal.wallis, libshuff, mantel, nmds, otu.association, parsimony, pca, pcoa, phylo.diversity, unifrac.unweighted, unifrac.weighted

OTU-Based Approaches commmands include: biom.info, classify.svm, collect.shared, collect.single, create.database, dist.shared, estimator.single, filter.shared, get.communitytype, get.coremicrobiome, get.group, get.groups, get.label, get.otus, get.otulist, get.oturep, get.otus, get.rabund, get.relabund, get.sabund, get.sharedseqs, heatmap.bin, heatmap.sim, lefse, list.otus, list.otus, make.clr, make.shared, merge.otus, metastats, normalize.shared, otu.hierarchy, primer.design, rarefaction.shared, rarefaction.single, remove.groups, remove.otus, remove.otus, remove.rare, sens.spec, sparcc, split.abund, summary.shared, summary.single, tree.shared, venn

Phylotype Analysis commmands include: classify.otu, classify.seqs, classify.tree, get.lineage, merge.taxsummary, remove.lineage, summary.tax

Sequence Processing commmands include: align.check, align.seqs, bin.seqs, chimera.bellerophon, chimera.ccode, chimera.check, chimera.perseus, chimera.pintail, chimera.slayer, chimera.uchime, chimera.vsearch, chop.seqs, cluster.fragments, consensus.seqs, count.groups, count.seqs, degap.seqs, deunique.seqs, dist.seqs, fastq.info, filter.seqs, get.mimarkspackage, get.seqs, list.seqs, make.contigs, make.fastq, make.lookup, make.sra, count.seqs, merge.sfffiles, pairwise.seqs, pcr.seqs, pre.cluster, remove.seqs, rename.seqs, reverse.seqs, screen.seqs, seq.error, sff.multiple, sff.info, shhh.flows, shhh.seqs, sort.seqs, split.groups, sra.info, sub.sample, summary.qual, summary.seqs, trim.flows, trim.seqs, unique.seqs

For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'

Common Questions:

1. How do I cite mothur?
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

2. Do you have an example analysis?
Yes, https://mothur.org/wiki/454_SOP and https://mothur.org/wiki/MiSeq_SOP highlight some of the things you can do with mothur.

3. Do you offer workshops?
Yes! Please see our https://mothur.org/wiki/Workshops page for more information.

4. What are mothur's file types?
Mothur uses and creates many file types. Including fasta, name, group, design, count, list, rabund, sabund, shared, relabund, oligos, taxonomy, constaxonomy, phylip, column, flow, qfile, file, biom and tree. You can find out more about these formats here: https://www.mothur.org/wiki/File_Types.

5. Is there a list of all of mothur's commands?
Yes! You can find it here, http://www.mothur.org/wiki/Category:Commands.

6. Why does the cutoff change when I cluster with average neighbor?
This is a product of using the average neighbor algorithm with a sparse distance matrix. When you run cluster, the algorithm looks for pairs of sequences to merge in the rows and columns that are getting merged together. Let's say you set the cutoff to 0.05. If one cell has a distance of 0.03 and the cell it is getting merged with has a distance above 0.05 then the cutoff is reset to 0.03, because it's not possible to merge at a higher level and keep all the data. All of the sequences are still there from multiple phyla. Incidentally, although we always see this, it is a bigger problem for people that include sequences that do not fully overlap.

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [https://github.com/mothur/mothur Mothur github]

=== System ===
64-bit Linux

Mothur-Sapelo2

2022-02-23T20:54:25Z

Keeko: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
1.43.0,1.45.2,1.47.0

=== Author / Distributor ===
Please see [https://mothur.org/wiki/ Mothur]

=== Description ===
"Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. The functionality of different software including dotur, sons, treeclimber, s-libshuff, unifrac, and others have been incorperated in Mothur. In addition to improving the flexibility of these software, a number of other features including calculators and visualization tools are available with Mothur."
More details, documentation and tutorials are at the[https://mothur.org/wiki/ Mothur Wiki]

=== Running Program ===
Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

The last version of this application is at /apps/eb/Mothur/1.47.0-GCCcore-8.3.0

To use this version, please load the module with
<pre class="gscript">
ml Mothur/1.47.0-GCCcore-8.3.0
</pre>
To run mother in "batch mode", collect your Mothur commands into a command file and use that file in a batch job. More information about creating Mothur batch files can be found here: https://mothur.org/wiki/batch_mode/
Some Mothur commands can use multiple cores. To use multiple cores, adjust the processors parameter for each command in the Mothur command file. You must also adjust the --cpus_per_task parameter in your submission script to be equal to the number of processors you request in your Mothur command file.

The following is an example of a Mothur command file requesting use of 8 cpus.This file is called Mother_Commandfile.txt, and assembles pair end reads and prepares them for analysis.

<pre class="gscript">
make.file(inputdir=./MiSeq_SOP, type=gz, prefix=stability)
make.contigs(file=current, processors=8)
screen.seqs(fasta=current, group=current, maxambig=0, maxlength=275)
unique.seqs()
count.seqs(name=current, group=current)
align.seqs(fasta=current, reference=silva.v4.fasta)
</pre>

The following is an example submission script using the above Mother command file.

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=Mothurtest # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task=8 # Use 8 cpus
#SBATCH --mem=10gb # Job memory request
#SBATCH --time=02:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x_%j.out # Standard output log
#SBATCH --error=%x_%j.err # Standard error log

#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu # Where to send mail

cd $SLURM_SUBMIT_DIR
module load mothur
mothur Mother_Commandfile.txt

</pre>

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Mothur/1.47.0-GCCcore-8.3.0
mothur --help
Linux version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at https://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Script Mode

mothur > help()

NOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.

Clustering commmands include: cluster, cluster.classic, cluster.fit, cluster.split, mgcluster, phylotype

General commmands include: get.current, get.dists, make.biom, make.file, make.group, make.lefse, merge.count, merge.files, merge.groups, remove.dists, rename.file, set.current, set.dir, set.logfile, set.seed, system

Hypothesis Testing commmands include: amova, anosim, clearcut, cooccurrence, corr.axes, deunique.tree, homova, indicator, kruskal.wallis, libshuff, mantel, nmds, otu.association, parsimony, pca, pcoa, phylo.diversity, unifrac.unweighted, unifrac.weighted

OTU-Based Approaches commmands include: biom.info, classify.svm, collect.shared, collect.single, create.database, dist.shared, estimator.single, filter.shared, get.communitytype, get.coremicrobiome, get.group, get.groups, get.label, get.otus, get.otulist, get.oturep, get.otus, get.rabund, get.relabund, get.sabund, get.sharedseqs, heatmap.bin, heatmap.sim, lefse, list.otus, list.otus, make.clr, make.shared, merge.otus, metastats, normalize.shared, otu.hierarchy, primer.design, rarefaction.shared, rarefaction.single, remove.groups, remove.otus, remove.otus, remove.rare, sens.spec, sparcc, split.abund, summary.shared, summary.single, tree.shared, venn

Phylotype Analysis commmands include: classify.otu, classify.seqs, classify.tree, get.lineage, merge.taxsummary, remove.lineage, summary.tax

Sequence Processing commmands include: align.check, align.seqs, bin.seqs, chimera.bellerophon, chimera.ccode, chimera.check, chimera.perseus, chimera.pintail, chimera.slayer, chimera.uchime, chimera.vsearch, chop.seqs, cluster.fragments, consensus.seqs, count.groups, count.seqs, degap.seqs, deunique.seqs, dist.seqs, fastq.info, filter.seqs, get.mimarkspackage, get.seqs, list.seqs, make.contigs, make.fastq, make.lookup, make.sra, count.seqs, merge.sfffiles, pairwise.seqs, pcr.seqs, pre.cluster, remove.seqs, rename.seqs, reverse.seqs, screen.seqs, seq.error, sff.multiple, sff.info, shhh.flows, shhh.seqs, sort.seqs, split.groups, sra.info, sub.sample, summary.qual, summary.seqs, trim.flows, trim.seqs, unique.seqs

For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'

Common Questions:

1. How do I cite mothur?
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

2. Do you have an example analysis?
Yes, https://mothur.org/wiki/454_SOP and https://mothur.org/wiki/MiSeq_SOP highlight some of the things you can do with mothur.

3. Do you offer workshops?
Yes! Please see our https://mothur.org/wiki/Workshops page for more information.

4. What are mothur's file types?
Mothur uses and creates many file types. Including fasta, name, group, design, count, list, rabund, sabund, shared, relabund, oligos, taxonomy, constaxonomy, phylip, column, flow, qfile, file, biom and tree. You can find out more about these formats here: https://www.mothur.org/wiki/File_Types.

5. Is there a list of all of mothur's commands?
Yes! You can find it here, http://www.mothur.org/wiki/Category:Commands.

6. Why does the cutoff change when I cluster with average neighbor?
This is a product of using the average neighbor algorithm with a sparse distance matrix. When you run cluster, the algorithm looks for pairs of sequences to merge in the rows and columns that are getting merged together. Let's say you set the cutoff to 0.05. If one cell has a distance of 0.03 and the cell it is getting merged with has a distance above 0.05 then the cutoff is reset to 0.03, because it's not possible to merge at a higher level and keep all the data. All of the sequences are still there from multiple phyla. Incidentally, although we always see this, it is a bigger problem for people that include sequences that do not fully overlap.

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [https://github.com/mothur/mothur Mothur github]

=== System ===
64-bit Linux

Mothur-Sapelo2

2022-02-23T20:42:00Z

Keeko: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.43.0,1.45.2,1.47.0 ===..."

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
1.43.0,1.45.2,1.47.0

=== Author / Distributor ===
Please see [https://mothur.org/wiki/ Mothur]

=== Description ===
"Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. The functionality of different software including dotur, sons, treeclimber, s-libshuff, unifrac, and others have been incorperated in Mothur. In addition to improving the flexibility of these software, a number of other features including calculators and visualization tools are available with Mothur."
More details, documentation and tutorials are at the[https://mothur.org/wiki/ Mothur Wiki]

=== Running Program ===
Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

The last version of this application is at /apps/eb/Mothur/1.47.0-GCCcore-8.3.0

To use this version, please load the module with
<pre class="gscript">
ml Mothur/1.47.0-GCCcore-8.3.0
</pre>
To run mother in "batch mode", collect your Mothur commands into a command file and use that file in a batch job. More information about creating Mothur batch files can be found here: https://mothur.org/wiki/batch_mode/
Some Mothur commands can use multiple cores. To use multiple cores, adjust the processors parameter for each command in the Mothur command file. You must also adjust the --cpus_per_task parameter in your submission script to be equal to the number of processors you request in your Mothur command file.

The following is an example of a Mothur command file requesting use of 8 cpus.This file is called Mother_Commandfile.txt, and assembles pair end reads and prepares them for analysis.

<pre class="gscript">
make.file(inputdir=./MiSeq_SOP, type=gz, prefix=stability)
make.contigs(file=current, processors=8)
screen.seqs(fasta=current, group=current, maxambig=0, maxlength=275)
unique.seqs()
count.seqs(name=current, group=current)
align.seqs(fasta=current, reference=silva.v4.fasta)
</pre>

The following is an example submission script using the above Mother command file.

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=Mothurtest # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task=8 # Use 8 cpus
#SBATCH --mem=10gb # Job memory request
#SBATCH --time=02:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x_%j.out # Standard output log
#SBATCH --error=%x_%j.err # Standard error log

#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu # Where to send mail

cd $SLURM_SUBMIT_DIR
module load mothur
mothur Mother_Commandfile.txt

</pre>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Mothur/1.47.0-GCCcore-8.3.0
mothur --help
Linux version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at https://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Script Mode

mothur > help()

NOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.

Clustering commmands include: cluster, cluster.classic, cluster.fit, cluster.split, mgcluster, phylotype

General commmands include: get.current, get.dists, make.biom, make.file, make.group, make.lefse, merge.count, merge.files, merge.groups, remove.dists, rename.file, set.current, set.dir, set.logfile, set.seed, system

Hypothesis Testing commmands include: amova, anosim, clearcut, cooccurrence, corr.axes, deunique.tree, homova, indicator, kruskal.wallis, libshuff, mantel, nmds, otu.association, parsimony, pca, pcoa, phylo.diversity, unifrac.unweighted, unifrac.weighted

OTU-Based Approaches commmands include: biom.info, classify.svm, collect.shared, collect.single, create.database, dist.shared, estimator.single, filter.shared, get.communitytype, get.coremicrobiome, get.group, get.groups, get.label, get.otus, get.otulist, get.oturep, get.otus, get.rabund, get.relabund, get.sabund, get.sharedseqs, heatmap.bin, heatmap.sim, lefse, list.otus, list.otus, make.clr, make.shared, merge.otus, metastats, normalize.shared, otu.hierarchy, primer.design, rarefaction.shared, rarefaction.single, remove.groups, remove.otus, remove.otus, remove.rare, sens.spec, sparcc, split.abund, summary.shared, summary.single, tree.shared, venn

Phylotype Analysis commmands include: classify.otu, classify.seqs, classify.tree, get.lineage, merge.taxsummary, remove.lineage, summary.tax

Sequence Processing commmands include: align.check, align.seqs, bin.seqs, chimera.bellerophon, chimera.ccode, chimera.check, chimera.perseus, chimera.pintail, chimera.slayer, chimera.uchime, chimera.vsearch, chop.seqs, cluster.fragments, consensus.seqs, count.groups, count.seqs, degap.seqs, deunique.seqs, dist.seqs, fastq.info, filter.seqs, get.mimarkspackage, get.seqs, list.seqs, make.contigs, make.fastq, make.lookup, make.sra, count.seqs, merge.sfffiles, pairwise.seqs, pcr.seqs, pre.cluster, remove.seqs, rename.seqs, reverse.seqs, screen.seqs, seq.error, sff.multiple, sff.info, shhh.flows, shhh.seqs, sort.seqs, split.groups, sra.info, sub.sample, summary.qual, summary.seqs, trim.flows, trim.seqs, unique.seqs

For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'

Common Questions:

1. How do I cite mothur?
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

2. Do you have an example analysis?
Yes, https://mothur.org/wiki/454_SOP and https://mothur.org/wiki/MiSeq_SOP highlight some of the things you can do with mothur.

3. Do you offer workshops?
Yes! Please see our https://mothur.org/wiki/Workshops page for more information.

4. What are mothur's file types?
Mothur uses and creates many file types. Including fasta, name, group, design, count, list, rabund, sabund, shared, relabund, oligos, taxonomy, constaxonomy, phylip, column, flow, qfile, file, biom and tree. You can find out more about these formats here: https://www.mothur.org/wiki/File_Types.

5. Is there a list of all of mothur's commands?
Yes! You can find it here, http://www.mothur.org/wiki/Category:Commands.

6. Why does the cutoff change when I cluster with average neighbor?
This is a product of using the average neighbor algorithm with a sparse distance matrix. When you run cluster, the algorithm looks for pairs of sequences to merge in the rows and columns that are getting merged together. Let's say you set the cutoff to 0.05. If one cell has a distance of 0.03 and the cell it is getting merged with has a distance above 0.05 then the cutoff is reset to 0.03, because it's not possible to merge at a higher level and keep all the data. All of the sequences are still there from multiple phyla. Incidentally, although we always see this, it is a bigger problem for people that include sequences that do not fully overlap.

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [https://github.com/mothur/mothur Mothur github]

=== System ===
64-bit Linux

Software

2022-02-23T18:57:36Z

Keeko:

,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-












| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-





| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
































| [[cryoSPARC-Sapelo2|cryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-










| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 4.5.6,2019.4,2020,2020.3,2021.2,2021.3,2021.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Mothur-Sapelo2|Mothur]] || 1.39.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 3.7.4, 2.7.16 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 3.5.0, 3.6.2, 4.0.0, 4.1.0 || [[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2020.28.61328, 2021.16.61629 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->































| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

































| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

NCBI Fasta-Sapelo2

2022-02-17T14:03:03Z

Keeko: edit typo

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

These fasta are updated at every first business day of the month.

Each fasta is located at the directory with the name pattern /db/ncbi/fasta/month-date-year,. For example, a database downloaded on May 1, 2017 would be located at /db/ncbi/fasta/05012017

The following databases are available:

<pre class="gscript">
est_human
est_mouse
est_others
nr
nt
htgs
gss
</pre>

Data source: [ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ NCBI Fasta FTP]

[[#top|Back to Top]]

Bioinformatics Databases

2022-02-17T14:02:28Z

Keeko: edit for clarity

As part of our services, the GACRC builds and hosts local copies of frequently cited application data, and provides assistance for sharing data among GACRC members. Datasets are located in the commonly shared "/db" filesystem. [[BLAST Databases-Sapelo2 | NCBI BLAST datasets]] are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.

NCBI BLAST Datasets can be loaded in the same way as software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:

<code>ml spider ncbiblastdb</code>

You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:

<code>module load ncbiblastdb/20210616</code>

Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
module load ncbiblastdb/20210616 
blastn -query example.fasta -out results.out -db nt 
</div>

In your actual submission script, use your own discretion for the Slurm header values.

NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

Various subject datasets, e.g. pfam, bowtie indexes of human and mouse, and NCBI bacterial datasets, are hosted as well. However, these datasets are not accessed with a module. These datasets either don’t need updating, the source does not update frequently, or the datasets are not used frequently by our users. These datasets will only be updated by user request.
Instead of using a module, to use these databases, use the path to the databases in your script. Below is an example using BLAST+ with a dataset not available as a module.

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
blastn -query example.fasta -out results.out -db /db/ncbiblast/refseq_microbial/fasta/09162020/ 
</div>

For datasets requested by individual lab groups, GACRC encourages users to maintain their own copies of databases, whose files can be installed in their group's shared "/work" area.
Similarly for datasets frequently updated by their source, the GACRC encourages users to maintain their own copies of these public databases.

The set of data which are regularly updated is open to review, and can be expanded based on available GACRC resources.

==Installed Bioinformatics Databases ==
{| border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" | Name
! scope="col" class="unsortable" | Version
! scope="col" | Module Available
|-
| akblab || 01/28/2018 || no
|-
| [[Bacteria NCBI-sapelo2|Bacteria NCBI]] || 12/21/2017 || no
|-
| [[bowtie2|hg19,mm10 & mm9]] || 07/29/2016 || no
|-
| cellranger || 10/29/2019 || no
|-
| conspred_ressources || 02/02/2017 || no
|-
| dammit || 03/18/2021 || no
|-
| deconseq || 12/01/2016 || no
|-
| decontaMiner-Sapelo2|decontaMiner || 08/29/2019 || no
|-
| eggnog-mapper || 04/16/2019 || no
|-
| funannotate || 08/15/2019 || no
|-
| DTDB-Tk || 01/15/2021 || no
|-
| hg || 09/20/2016 || no
|-
| kegg || 09/09/2016 || no
|-
| maker || 05/22/2018 || no
|-
| MetaCLADE || 08/29/2019 || no
|-
| [[BLAST Databases-Sapelo2 | NCBI BLAST Databases]] || beginning of every month || yes
|-
| [[NCBI Fasta-Sapelo2|NCBI Fasta]] || beginning of every month || yes
|-
| ngs || 11/03/2016 || no
|-
| nndb || 04/29/2020 || no
|-
| PB || 04/24/2019 || no
|-
| [[PfamDB-Sapelo2|pfam]] || 10/07/2021 || no
|-
| pylosift || 07/20/2020 || no
|-
| [[Refseq-Sapelo2|Refseq_genomic]] || || no
|-
| repbase || 01/09/2017 || no
|-
| rfam || 02/09/2017 || no
|-
| seqdb || 05/23/2019 || no
|-
| sortmerna || 02/02/2021 || no
|-
| [[TaxDB-Sapelo2|TaxDB]] || 02/26/2019 || no
|-
| topcons2 || 02/18/2021 || no
|-
| [[Uniprot-Sapelo2|Uniprot]] || 11/19/2020 || no
|-
| [[Uniref-Sapelo2|Uniref]] || 06/28/2018 || no
|-
| [[wublast-Sapelo2|wublast]] || 03/01/2020 || no
|-
|}

BLAST Databases-Sapelo2

2022-02-17T14:01:15Z

Keeko: edits for clarity and typo in date

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

'''Blast databases'''

Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with the name pattern /db/ncbiblasty/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.

NCBI BLAST Datasets can be loaded just like software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:

<code>ml spider ncbiblastdb</code>

You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:

<code>module load ncbiblastdb/20210616</code>

Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
module load ncbiblastdb/20220201 
blastn -query example.fasta -out results.out -db nt 
</div>

In your actual submission script, use your own discretion for the Slurm header values.

NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

'''Blast database - old version 5'''

According to https://ncbiinsights.ncbi.nlm.nih.gov/tag/blastdbv5/, around Feb. 04, 2020 NCBI dropped the _v5 suffix for the v5 Blast databases.

An old version of the v5 database (download in June 2019) is located at a directory with name pattern as /db/ncbiblast.v5/''dbname'', where ''dbname'' is the name of the database, such as nr, nt, taxdb, refseq_rna, swissprot, etc.

These old versions of the nr and nt databases still have the _v5 suffix, i.e. they are called nr_v5 and nt_v5, respectively.

[[#top|Back to Top]]

NCBI Fasta-Sapelo2

2022-02-17T05:26:46Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

These fasta are updated at every first business day of the month.

Each fasta is located at the directory with name pattern as /db/ncbi/fasta/month-date-year,. For example, a database downloaded on May 1, 2017 would be located at /db/ncbi/fasta/05012017

The following databases are available:

<pre class="gscript">
est_human
est_mouse
est_others
nr
nt
htgs
gss
</pre>

Data source: [ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ NCBI Fasta FTP]

[[#top|Back to Top]]

Bioinformatics Databases

2022-02-17T05:21:02Z

Keeko:

As part of our services, the GACRC builds and hosts local copies of frequently cited application data, and provides assistance for sharing data among GACRC members. Datasets are located in the commonly shared "/db" filesystem. [[BLAST Databases-Sapelo2 | NCBI BLAST datasets]] are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.

NCBI BLAST Datasets can be loaded in a similar way to software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:

<code>ml spider ncbiblastdb</code>

You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:

<code>module load ncbiblastdb/20210616</code>

Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
module load ncbiblastdb/20210616 
blastn -query example.fasta -out results.out -db nt 
</div>

In your actual submission script, use your own discretion for the Slurm header values.

NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

Various subject datasets, e.g. pfam, bowtie indexes of human and mouse, and NCBI bacterial datasets, are hosted as well. However, these datasets are not accessed with a module. These datasets either don’t need updating, the source does not update frequently, or the datasets are not used frequently by our users. These datasets will only be updated by user request.
Instead of using a module, to use these databases, use the path to the databases in your script. Below is an example using BLAST+ with a dataset not available as a module.

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
blastn -query example.fasta -out results.out -db /db/ncbiblast/refseq_microbial/fasta/09162020/ 
</div>

For datasets requested by individual lab groups, GACRC encourages users to maintain their own copies of databases, whose files can be installed in their group's shared "/work" area.
Similarly for datasets frequently updated by their source, the GACRC encourages users to maintain their own copies of these public databases.

The set of data which are regularly updated is open to review, and can be expanded based on available GACRC resources.

==Installed Bioinformatics Databases ==
{| border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" | Name
! scope="col" class="unsortable" | Version
! scope="col" | Module Available
|-
| akblab || 01/28/2018 || no
|-
| [[Bacteria NCBI-sapelo2|Bacteria NCBI]] || 12/21/2017 || no
|-
| [[bowtie2|hg19,mm10 & mm9]] || 07/29/2016 || no
|-
| cellranger || 10/29/2019 || no
|-
| conspred_ressources || 02/02/2017 || no
|-
| dammit || 03/18/2021 || no
|-
| deconseq || 12/01/2016 || no
|-
| decontaMiner-Sapelo2|decontaMiner || 08/29/2019 || no
|-
| eggnog-mapper || 04/16/2019 || no
|-
| funannotate || 08/15/2019 || no
|-
| DTDB-Tk || 01/15/2021 || no
|-
| hg || 09/20/2016 || no
|-
| kegg || 09/09/2016 || no
|-
| maker || 05/22/2018 || no
|-
| MetaCLADE || 08/29/2019 || no
|-
| [[BLAST Databases-Sapelo2 | NCBI BLAST Databases]] || beginning of every month || yes
|-
| [[NCBI Fasta-Sapelo2|NCBI Fasta]] || beginning of every month || yes
|-
| ngs || 11/03/2016 || no
|-
| nndb || 04/29/2020 || no
|-
| PB || 04/24/2019 || no
|-
| [[PfamDB-Sapelo2|pfam]] || 10/07/2021 || no
|-
| pylosift || 07/20/2020 || no
|-
| [[Refseq-Sapelo2|Refseq_genomic]] || || no
|-
| repbase || 01/09/2017 || no
|-
| rfam || 02/09/2017 || no
|-
| seqdb || 05/23/2019 || no
|-
| sortmerna || 02/02/2021 || no
|-
| [[TaxDB-Sapelo2|TaxDB]] || 02/26/2019 || no
|-
| topcons2 || 02/18/2021 || no
|-
| [[Uniprot-Sapelo2|Uniprot]] || 11/19/2020 || no
|-
| [[Uniref-Sapelo2|Uniref]] || 06/28/2018 || no
|-
| [[wublast-Sapelo2|wublast]] || 03/01/2020 || no
|-
|}

BLAST Databases-Sapelo2

2022-02-17T05:18:38Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

'''Blast databases'''

Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with name pattern as /db/ncbiblasty/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.

NCBI BLAST Datasets can be loaded in a similar way to software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:

<code>ml spider ncbiblastdb</code>

You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:

<code>module load ncbiblastdb/20210616</code>

Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
module load ncbiblastdb/20210616 
blastn -query example.fasta -out results.out -db nt 
</div>

In your actual submission script, use your own discretion for the Slurm header values.

NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

'''Blast database - old version 5'''

According to https://ncbiinsights.ncbi.nlm.nih.gov/tag/blastdbv5/, around Feb. 04, 2020 NCBI dropped the _v5 suffix for the v5 Blast databases.

An old version of the v5 database (download in June 2019) is located at a directory with name pattern as /db/ncbiblast.v5/''dbname'', where ''dbname'' is the name of the database, such as nr, nt, taxdb, refseq_rna, swissprot, etc.

These old versions of the nr and nt databases still have the _v5 suffix, i.e. they are called nr_v5 and nt_v5, respectively.

[[#top|Back to Top]]

BLAST Databases-Sapelo2

2022-02-17T05:17:30Z

Keeko: removed reference to redundant /db/ncbiblast databases organized by name. Added more info about loading databases with modules

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

'''Blast databases'''

Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with name pattern as /db/ncbiblasty/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.

NCBI BLAST Datasets can be loaded in a similar way to software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:

<code>ml spider ncbiblastdb</code>

You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:

<code>module load ncbiblastdb/20210616</code>

Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:

NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

'''Blast database - old version 5'''

According to https://ncbiinsights.ncbi.nlm.nih.gov/tag/blastdbv5/, around Feb. 04, 2020 NCBI dropped the _v5 suffix for the v5 Blast databases.

An old version of the v5 database (download in June 2019) is located at a directory with name pattern as /db/ncbiblast.v5/''dbname'', where ''dbname'' is the name of the database, such as nr, nt, taxdb, refseq_rna, swissprot, etc.

These old versions of the nr and nt databases still have the _v5 suffix, i.e. they are called nr_v5 and nt_v5, respectively.

[[#top|Back to Top]]

BLAST Databases-Sapelo2

2022-02-17T05:06:27Z

Keeko: added more clarity on what a blast db is and that refseq_genomic is unavailable.

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

'''Blast database'''

Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with name pattern as /db/ncbiblast/''dbname''/''month-day-year'', where ''dbname'' is the name of the database, such as nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome, swissprot, etc. The database refseq_genomic is no longer available to download as a pre-formatted database.

For example, an nr database downloaded on June 04, 2020 will be available in /db/ncbiblast/nr/06042020.

Available databases:
<pre class="gscript">
/db/ncbiblast/human_genome/03012021
/db/ncbiblast/mouse_genome/03012021
/db/ncbiblast/nr/03012021
/db/ncbiblast/nt/03012021
/db/ncbiblast/refseq_rna/03012021
/db/ncbiblast/refseq_protein/03012021
/db/ncbiblast/swissprot/03012021
/db/ncbiblast/taxdb/03012021
</pre>

'''Blast database - old version 5'''

According to https://ncbiinsights.ncbi.nlm.nih.gov/tag/blastdbv5/, around Feb. 04, 2020 NCBI dropped the _v5 suffix for the v5 Blast databases.

An old version of the v5 database (download in June 2019) is located at a directory with name pattern as /db/ncbiblast.v5/''dbname'', where ''dbname'' is the name of the database, such as nr, nt, taxdb, refseq_rna, swissprot, etc.

These old versions of the nr and nt databases still have the _v5 suffix, i.e. they are called nr_v5 and nt_v5, respectively.

[[#top|Back to Top]]

Bioinformatics Databases

2022-02-17T05:01:24Z

Keeko: clearer description of NCBI BLAST databases

As part of our services, the GACRC builds and hosts local copies of frequently cited application data, and provides assistance for sharing data among GACRC members. Datasets are located in the commonly shared "/db" filesystem. NCBI BLAST datasets are pre-formatted to work with BLAST and BLAST+ and are located in "/db/ncbiblast/" and are organized by date.

NCBI BLAST Datasets can be loaded in a similar way to software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:

<code>ml spider ncbiblastdb</code>

You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:

<code>module load ncbiblastdb/20210616</code>

Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
module load ncbiblastdb/20210616 
blastn -query example.fasta -out results.out -db nt 
</div>

In your actual submission script, use your own discretion for the Slurm header values.

NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every month as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

Various subject datasets, e.g. pfam, bowtie indexes of human and mouse, and NCBI bacterial datasets, are hosted as well. However, these datasets are not accessed with a module. These datasets either don’t need updating, the source does not update frequently, or the datasets are not used frequently by our users. These datasets will only be updated by user request.
Instead of using a module, to use these databases, use the path to the databases in your script. Below is an example using BLAST+ with a dataset not available as a module.

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
blastn -query example.fasta -out results.out -db /db/ncbiblast/refseq_microbial/fasta/09162020/ 
</div>

For datasets requested by individual lab groups, GACRC encourages users to maintain their own copies of databases, whose files can be installed in their group's shared "/work" area.
Similarly for datasets frequently updated by their source, the GACRC encourages users to maintain their own copies of these public databases.

The set of data which are regularly updated is open to review, and can be expanded based on available GACRC resources.

==Installed Bioinformatics Databases ==
{| border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" | Name
! scope="col" class="unsortable" | Version
! scope="col" | Module Available
|-
| akblab || 01/28/2018 || no
|-
| [[Bacteria NCBI-sapelo2|Bacteria NCBI]] || 12/21/2017 || no
|-
| [[bowtie2|hg19,mm10 & mm9]] || 07/29/2016 || no
|-
| cellranger || 10/29/2019 || no
|-
| conspred_ressources || 02/02/2017 || no
|-
| dammit || 03/18/2021 || no
|-
| deconseq || 12/01/2016 || no
|-
| decontaMiner-Sapelo2|decontaMiner || 08/29/2019 || no
|-
| eggnog-mapper || 04/16/2019 || no
|-
| funannotate || 08/15/2019 || no
|-
| DTDB-Tk || 01/15/2021 || no
|-
| hg || 09/20/2016 || no
|-
| kegg || 09/09/2016 || no
|-
| maker || 05/22/2018 || no
|-
| MetaCLADE || 08/29/2019 || no
|-
| [[BLAST Databases-Sapelo2 | NCBI BLAST Databases]] || beginning of every month || yes
|-
| [[NCBI Fasta-Sapelo2|NCBI Fasta]] || beginning of every month || yes
|-
| ngs || 11/03/2016 || no
|-
| nndb || 04/29/2020 || no
|-
| PB || 04/24/2019 || no
|-
| [[PfamDB-Sapelo2|pfam]] || 10/07/2021 || no
|-
| pylosift || 07/20/2020 || no
|-
| [[Refseq-Sapelo2|Refseq_genomic]] || || no
|-
| repbase || 01/09/2017 || no
|-
| rfam || 02/09/2017 || no
|-
| seqdb || 05/23/2019 || no
|-
| sortmerna || 02/02/2021 || no
|-
| [[TaxDB-Sapelo2|TaxDB]] || 02/26/2019 || no
|-
| topcons2 || 02/18/2021 || no
|-
| [[Uniprot-Sapelo2|Uniprot]] || 11/19/2020 || no
|-
| [[Uniref-Sapelo2|Uniref]] || 06/28/2018 || no
|-
| [[wublast-Sapelo2|wublast]] || 03/01/2020 || no
|-
|}

NCBI Fasta-Sapelo2

2022-02-01T17:11:40Z

Keeko: more clear wording

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

These fasta are updated at every first business day of the month.

Each fasta is located at directory with name pattern as /db/ncbi/fasta/month-date-year,. For example, a database downloaded on May 1, 2017 would be located at /db/ncbi/fasta/05012017

<pre class="gscript">
est_human
est_mouse
est_others
nr
nt
htgs
gss
</pre>

Data source: [ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ NCBI Fasta FTP]

[[#top|Back to Top]]

Training

2022-02-01T02:26:25Z

Keeko: /* R Basics */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==
In '''February''' 2022, the GACRC is hosting ten training sessions (Sapelo2 cluster new user training, Linux basics, R basics, and Python basics).

We offer:

1. Linux training for Linux-inexperienced cluster new users (3 sessions)

2. Sapelo2 cluster new user training (3 sessions)

3. R basics (2 sessions)

4. Python basics (2 sessions)

'''Please Note:''' The training workshops will be offered remotely via Zoom Meeting. Detailed information on how to join the Zoom meeting will be sent to your UGA email account prior to each training session.

==Event Schedule==

===Sapelo2 Cluster New User Training===

Our Sapelo2 training consists of 1 hr 30 mins of instructional videos, followed by a 1 hr 30 min workshop. '''The instructional videos are required to be viewed prior to the training workshop, and they can be found [https://kaltura.uga.edu/playlist/dedicated/176125031/1_4o12v8b4/1_9zi68rgi here]'''

'''Prerequisites:'''

* Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Video Playlist Training Goals:'''

* Understand the layout of Sapelo2

* Understand the Sapelo2 file systems

* Understand the Sapelo2 partitions

* Understand the Sapelo2 software environment

'''Workshop Training Goals:'''

* Understand how to request computing resources and submit a computational batch job following the Sapelo2 cluster general workflow

* Understand how to initiate an interactive job

* Understand how to transfer files to and from the cluster

* Understand how to get support from GACRC support team when you have any issues on cluster

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Using Sapelo2 Cluster at the GACRC||February 3, Thursday, 1:00 PM - 2:30 PM
|-
|Using Sapelo2 Cluster at the GACRC||February 9, Wednesday, 1:00 PM - 2:30 PM
|-
|Using Sapelo2 Cluster at the GACRC||February 25, Friday, 1:00 PM - 2:30 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites

'''Training Goals:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Use Linux on Cluster||February 1, Tuesday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster||February 7, Monday, 1:00 PM - 3:00 PM
|-
|Use Linux on Cluster||February 23, Wednesday, 1:00 PM - 3:00 PM
|-
|}

===Sapelo2 Cluster Advanced Topics===
'''Prerequisites:'''
* Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.
* Sapelo2 cluster new user training. Fundamental HPC and Sapelo2 knowledge is required for this advanced Sapelo2 workshop.

'''Training Goals:'''

1. Understand HPC Conceptual Framework

2. Investigate Sapelo2 HPC resources by using sinfo, sinfo-nodes, scontrol show, sacctmgr show, etc.

3. Understand how to request computing resources on memory, CPU cores, and GPU device for your jobs

4. Understand how to use local scratch storage to improve job IO performance

5. Learn about new MPI libraries and how to compile/run MPI jobs on Sapelo2

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Sapelo2 Cluster Advanced Topics||Not scheduled in February
|-
|}

===Python Basics===
'''Prerequisite:''' No prerequisites

'''Training Goals:'''

1. Understand Python scientific modules and distributions

2. Understand Python general lexical conventions; Python built-in data types, like string, list, tuple, dictionary, etc.

3. Understand Python programming structures and procedural programming using functions

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Title
! scope="col" |Date/Time
|-
|Python Basics I||February 15, Tuesday, 1:00 PM - 3:00 PM
|-
|Python Basics II||February 17, Thursday, 1:00 PM - 3:00 PM
|-
|}

===R Basics===
'''Prerequisite:''' No prerequisites

'''Training Goals:'''

1. Understand fundamentals of R language, e.g. R general lexical conventions, data types, functions, and packages. Part 2 will introduce loops and functions.

2. Be able to manipulate and create data frames using built in functions and the dplyr package.

3. Interact with your file system and submit R code as a batch job to Sapelo 2.

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
| R Basics I||February 8, Tuesday 1:00 PM - 3:00 PM
|-
|R Basics II||February 10, Thursday, 1:00 PM - 3:00 PM
|-
|}

===Conda===
'''Prerequisite:''' No prerequisites

'''Training Goals:'''

1. Understand fundamentals of conda environment

2. Use conda to create and configure your own virtual environments

3. Activate your environments to run python apps from your home directory on Sapelo2

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" |Title
! scope="col" |Date/Time
|-
|Conda Basics||Not scheduled in February
|-
|}

==How to Register==

'''Please Note''', the training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are '''ONLY''' offered to '''new users''' who need computing user accounts on the GACRC Sapelo2 cluster, or any current users who have never attended the GACRC Sapelo2 cluster new user training before. Please ask your group PI/UGA faculty member to send us a request for you, using the GACRC User Account Request form at https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839

If you want to attend '''Python Basics''', '''R''', and '''Conda basics''' training sessions, please send us a request using the GACRC Training Request form at https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 . In your request, please tell us which session(s) you want to attend.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at https://gacrc.uga.edu/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

== Topic Introduction==

Title: '''Sap2test cluster migration training'''

Focus: Slurm queueing system, including Slurm job commands, job environment variables, and job submission headers, etc.

The new software environment on Sap2test

Other important topics related to Sap2test working environment

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 HPC cluster and computational batch job submission workflow

Cluster's storage environment

Computational queues on cluster

Software environment

How to submit computational batch jobs

Other tips and guidelines for users

Title: '''Sapelo2 Cluster Advanced Topics'''

Focus: More advanced topics on how to use Sapelo2 cluster

Understand HPC Conceptual Framework

Investigate Sapelo2 HPC resources by using sinfo, sinfo-nodes, scontrol show, sacctmgr show, etc.

Understand how to request computing resources on memory, CPU cores, and GPU device for your jobs

Understand ow to use local scratch storage to improve job IO performance

Learn about New MPI libraries and how to compile/run MPI jobs on Sapelo2

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common commands, filesystem, and shell

Linux shell scripting basics

Common Linux utilities, e.g., grep, sed, find, sort, and awk, etc.

Linux Hands-on practice

Title: '''Python Basics I, II'''

Focus of I: Python language overview, scientific modules and distributions

Python general lexical conventions

Basic built-in data types, like string, list, tuple, dictionary, etc.

Focus of II: Programming structures: control flow and loop

Function: procedural programming with examples, lambda expression, factory function and generator

Title: '''R Basics I, II'''

Focus of I: R language overview,general lexical conventions, data types, functions, and packages.

Basic built-in data types, like string, numeric, list, dataframe etc. Using the dplyr package.

Focus of II: Programming structures: control flow, loops and functions

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Install Python packages/modules in a user's home directory on Sapelo2 cluster

Python versions installed on Sapelo2

Python environment details on Sapelo2

How to know a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''Do It Yourself: Using Conda to create and run python environments to suit your computing needs effortlessly!'''

Focus: Use conda to create and configure your own python virtual environments; Activate your environments to run python apps from your home directory on Sapelo2

What is Conda and its environment

Conda on Sapelo2

Use conda to create and configure your own python virtual environments

Activate your environments to run python apps from your home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

==Download==

====Sapelo2 Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_Sapelo2_cluster_new_user_training_workshop_v10.7.pdf]]
|-
|}

====Sap2test Migration Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Migrating_to_Slurm_and_new_software_environment.pdf]]
|}

'''Please note:''' To help users familiarize with Slurm and the test cluster environment, we have prepared some training videos that are available from the '''GACRC's Kaltura channel''' at
https://kaltura.uga.edu/channel/GACRC/176125031 (login with MyID and password is required).

==== Teaching Cluster Training====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:GACRC_Teaching_cluster_new_user_training_workshop_v5.2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Linux_Training_For_New_Users_Of_Cluster_Suchi_04252019.pdf]]
|-
|}

==== Python Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Python_Language_Basics_I_v5.1.pdf]]
|-
|[[Media:Python_Language_Basics_II_v5.1.pdf]]
|-
|}

====R Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:R Language Basics PowerPoint v2.0.1.pdf|Media:R_Language_Basics_PowerPoint_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_Document_v2.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Powerpoint_v1.0.pdf]]
|-
|[[Media:R_Language_Basics_part_2_Document_v1.0.pdf]]
|-
|}

====Perl Basics====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
|[[Media:Perl_Language_Basics_I_Workshop_v1.pdf]]
|-
|}

====Topical Sessions====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|
|-
| [[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics_v1.pdf]]
|-
| [[Media:Using_Conda_on_the_GACRC_Sap2test_cluster_v1.pdf]]
|-
|[[Media:Blast_Workshop_GACRC_02012017.pdf]]
|-
|[[Media:Next-Generation_Sequencing_Applications_at_GACRC_10282016.pdf]]
|-
|}

==== Out-Reach/On-Class Talk====

{| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" |Workshop PDF
|-
|PHYS8601 - Spring2022||On-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]]
|-
|PHYS4601/6601 - Spring2022||On-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] ; [[Media:Gacrc_handout2021_phys4601.pdf]]
|-
|PHYS8602 - Spring2021||On-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602-2021.pdf]] ; [[Media:Gacrc_handout2021_phys8602.pdf]]
|-
|GENE4220 - Fall2020||On-Class||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_GENE4220_Fall2020.pdf]]
|-
|College of Veterinary Medicine - Spring2020||Out-Reach (jlslab) ||[[Media:Using_GACRC_Sapelo2_Cluster-Advanced_Topics(1).pdf]]
|-
|Byod Data Center - Fall2019||On-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Cluster.pdf]]
|-
| Department of Linguistics - Fall2019||On-class (LING6570)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop_LING6570_Part2.pdf]]
|-
|The Center for Simulational Physics - Fall2019 ||Out-Reach (Seminar Talk 20190820)||[[Media:Introduction_to_GACRC_Computing_Facility_-_Sapelo2_Cluster_CSP-Fall2019.pdf]]
|-
|The Center for Simulational Physics||On-Class (PHYS4601/6601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys4601.pdf]] [[Media:Gacrc_handout2019_phys4601.pdf]]
|-
|The Center for Simulational Physics||On-Class (PHYS8601)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8601.pdf]] [[Media:Gacrc_handout2020_phys8601.pdf]]
|-
|The Center for Simulational Physics ||On-Class (PHYS8602)||[[Media:GACRC_Teaching_cluster_new_user_training_workshop-phys8602.pdf]] [[Media:Gacrc_handout2019_phys8602.pdf]]
|-
|Food Science - Fall2018 ||On-Class (FYOS1001)||[[Media:High_Performance_Computing_(HPC)_on_Sapelo2_Cluster_at_GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer2018||Out-Reach (Seminar Talk 20180821)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
| Miller plant science - Summer2018 ||Out-Reach (jlmlab)||[[Media:Introduction_to_GACRC_Sapelo2_cluster.pdf]]
|-
|Biochemistry and Molecular Biology - Spring2018||On-Class (BCMB8330)||[[Media:GACRC_zcluster_Class_Training_BCMB8330_Spring_2018.pdf]]
|-
| The Center for Simulational Physics - Summer2017||Out-Reach (Seminar Talk 20170831) ||[[Media:Introduction_on_HPC_Resources_at_the_GACRC.pdf]]
|-
|Computational Physics - Spring2017||On-class (PHYS4601/6601) ||[[Media:Phys4601.pdf]]
|-
|Computational Physics - Spring2017||On-class (PHYS8602)||[[Media:Phys8602.pdf]]
|-
|The Institute of Bioinformatics and the Quantitative Biology Consulting Group|| Out-Reach||[[Media:Introduction_to_HPC_Resources_at_GACRC_BBB_Talk_20151014.pdf]]
|-
|The Center for Simulational Physics|| Out-Reach (Seminar Talk 20160906)||[[Media:Introduction_to_Sapelo_Computing_Resources_at_GACRC_Workshop20160906.pdf]]
|-
|Microbiology||On-Class (MIBO8150) ||[[Media:Introduction_to_HPC_Resources_at_GACRC_MIBO8150_20160926.pdf]]
|-
|Statistics||On-Class (STAT8060)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_Workshop_STAT8060_20150826.pdf]]
|-
|Biochemistry and Molecular Biology||On-Class (BCMB8211) ||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BCMB8211_20160114.pdf]]
|-
|Plant Biology||On-Class (PBIO/BINF8350)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO-BINF8350_20160115.pdf]]
|-
|Plant Biology - Bioinformatics Applications Fall2016||On-Class (PBIO4550)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_PBIO_4550_08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall2016||On-Class (BINF4005)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_BINF_4005_08312016.pdf]]
|-
|Computers in Experimental Genetics Fall2016||On-Class (GENE4220)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_GENE_4220_10192016.pdf]]
|-
|Statistics - Advanced Applications and Computing in R Fall2016||On-Class (STAT8330)||[[Media:Introduction_to_HPC_Using_zcluster_at_GACRC_STAT8330_11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

== Past Sessions ==

[[Pass Sessions in 2021]]

[[Past Sessions in 2020]]

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Structure-Sapelo2

2022-02-01T01:24:59Z

Keeko: added info about mainparams and extraparams file

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
2.3.4

=== Author / Distributor ===

[http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== Description ===
"The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. "
More details are at [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

The latest version is at /apps/eb/structure/2.3.4-foss-2019b

To use this program, please first load its module with
<pre class="gcommand">
module load structure/2.3.4-foss-2019b
</pre>

To run STUCTURE you will need both a mainparams file and an extraparams file. These two files contain program parameters which are set by the user, and are read every time the program executes. Make sure both of those files are in your working directory when you use structure. You can also specify those files with the -m (mainparams) and -e (extraparams) options to the structure command.

More about the mainparams and extraparams file can be found here:

<nowiki>https://web.stanford.edu/group/pritchardlab/software/readme/node32.html</nowiki>

Examples of the mainparams file and extraparams file which you can use as templates can be found at /apps/eb/structure/2.3.4-foss-2019b/mainparams and /apps/eb/structure/2.3.4-foss-2019b/extraparams respectively.

Here is an example of a shell script sub.sh to run on at the batch queue:
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash <nowiki>#</nowiki>SBATCH --job-name=structurejob <nowiki>#</nowiki>SBATCH --partition=batch <nowiki>#</nowiki>SBATCH --mail-type=ALL <nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu

<nowiki>#</nowiki>SBATCH --ntasks=1 <nowiki>#</nowiki>SBATCH --mem=10gb <nowiki>#</nowiki>SBATCH --time=08:00:00 <nowiki>#</nowiki>SBATCH --output=structurejob.%j.out <nowiki>#</nowiki>SBATCH --error=structurejob.%j.err 

cd $SLURM_SUBMIT_DIR module load structure/2.3.4-foss-2019b 

structure [options]
</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. And [options] should be replaced by any options you want to use.

Here is an example of job submission
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">

module load structure/2.3.4-foss-2019b
structure -h
----------------------------------------------------
STRUCTURE by Pritchard, Stephens and Donnelly (2000)
and Falush, Stephens and Pritchard (2003)
Code by Pritchard, Falush and Hubisz
Version 2.3.4 (Jul 2012)
----------------------------------------------------

Reading file "mainparams".
datafile is
infile
Reading file "extraparams".
Note: RANDOMIZE is set to 1. The random number generator will be initialized using the system clock, ignoring any specified value of SEED.
Unable to open the file infile.

Exiting the program due to error(s) listed above.
</pre>
[[#top|Back to Top]]

=== Installation ===

source code from [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== System ===
64-bit Linux

Structure-Sapelo2

2022-02-01T01:16:43Z

Keeko: minor page formatting

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
2.3.4

=== Author / Distributor ===

[http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== Description ===
"The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. "
More details are at [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

The latest version is at /apps/eb/structure/2.3.4-foss-2019b

To use this program, please first load its module with
<pre class="gcommand">
module load structure/2.3.4-foss-2019b
</pre>

Here is an example of a shell script sub.sh to run on at the batch queue:
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash <nowiki>#</nowiki>SBATCH --job-name=structurejob <nowiki>#</nowiki>SBATCH --partition=batch <nowiki>#</nowiki>SBATCH --mail-type=ALL <nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu

<nowiki>#</nowiki>SBATCH --ntasks=1 <nowiki>#</nowiki>SBATCH --mem=10gb <nowiki>#</nowiki>SBATCH --time=08:00:00 <nowiki>#</nowiki>SBATCH --output=structurejob.%j.out <nowiki>#</nowiki>SBATCH --error=structurejob.%j.err 

cd $SLURM_SUBMIT_DIR module load structure/2.3.4-foss-2019b 

structure [options]
</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. And [options] should be replaced by any options you want to use.

Here is an example of job submission
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">

module load structure/2.3.4-foss-2019b
structure -h
----------------------------------------------------
STRUCTURE by Pritchard, Stephens and Donnelly (2000)
and Falush, Stephens and Pritchard (2003)
Code by Pritchard, Falush and Hubisz
Version 2.3.4 (Jul 2012)
----------------------------------------------------

Reading file "mainparams".
datafile is
infile
Reading file "extraparams".
Note: RANDOMIZE is set to 1. The random number generator will be initialized using the system clock, ignoring any specified value of SEED.
Unable to open the file infile.

Exiting the program due to error(s) listed above.
</pre>
[[#top|Back to Top]]

=== Installation ===

source code from [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== System ===
64-bit Linux

Structure-Sapelo2

2022-02-01T01:12:31Z

Keeko: created STRUCTURE page

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
2.3.4

=== Author / Distributor ===

[http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== Description ===
"The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. "
More details are at [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== Running Program ===

Also refer to [[Running Jobs on the teaching cluster]]

The last version is at /apps/eb/structure/2.3.4-foss-2019b

To use this program, please first load its module with
<pre class="gcommand">
module load structure/2.3.4-foss-2019b
</pre>

Here is an example of a shell script sub.sh to run on at the batch queue:
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=structurejob 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=structurejob.%j.out 
<nowiki>#</nowiki>SBATCH --error=structurejob.%j.err 

cd $SLURM_SUBMIT_DIR 
module load structure/2.3.4-foss-2019b 
 
structure [options] 
</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. And [options] should be replaced by any options you want to use.

Here is an example of job submission
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">

module load structure/2.3.4-foss-2019b
structure -h
----------------------------------------------------
STRUCTURE by Pritchard, Stephens and Donnelly (2000)
and Falush, Stephens and Pritchard (2003)
Code by Pritchard, Falush and Hubisz
Version 2.3.4 (Jul 2012)
----------------------------------------------------

Reading file "mainparams".
datafile is
infile
Reading file "extraparams".
Note: RANDOMIZE is set to 1. The random number generator will be initialized using the system clock, ignoring any specified value of SEED.
Unable to open the file infile.

Exiting the program due to error(s) listed above.
</pre>
[[#top|Back to Top]]

=== Installation ===

source code from [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== System ===
64-bit Linux

Software

2022-02-01T01:09:49Z

Keeko: added STRUCTURE row

,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-












| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-





| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

































|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-










| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 4.5.6,2019.4,2020,2020.3,2021.2,2021.3,2021.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
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|- -->






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|- -->







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|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
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|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
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| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
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[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

GROMACS-Sapelo2

2022-01-25T19:34:28Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6, 2019.4, 2020, 2020.3, 2021.2, 2021.3, 2021.4

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE) David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-fosscuda-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020.3-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-fosscuda-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.2-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-fosscuda-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.3-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-fosscuda-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.4-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-fosscuda-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or P100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

If using a P100 GPU node, it is advised to request all 32 CPUs there. If running an older version of GROMACS (up to 2021.3) on a K40 node, it is advised to request a low number of CPUs (~ 4), to leave enough CPUs for other GPU jobs to use the other K40 cards on the node.



Sample job submission script sub.sh to run v. 2021.3 and use 4 CPU cores on one node and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --gres=gpu:K40:1 # Request one K40 gpu
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task = 4 # 4cpus per task
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

gmx mdrun [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testgromacs''' should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node(--cpus-per-task), a suitable wall time (the example above specifies 4 hours), and a suitable amount of memory.

Sample job submission script using MPI and OpenMP to run v. 2021.3 and use 4 CPU cores per task and 2 GPU K40 cards:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --gres=gpu:K40:2 # Request one K40 gpu
#SBATCH --ntasks=2 # Run on a single CPU
#SBATCH --cpus-per-task = 4 # 4cpus per task
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

mpirun -np 2 gmx_mpi mdrun [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. Make sure the number of GPUS requested is equal to the number of tasks requested(--ntasks). The job name '''testgromacs''' should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node(--cpus-per-task), a suitable wall time (the example above specifies 4 hours), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-25T18:55:40Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6, 2019.4, 2020, 2020.3, 2021.2, 2021.3, 2021.4

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE) David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-fosscuda-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020.3-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-fosscuda-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.2-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-fosscuda-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.3-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-fosscuda-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.4-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-fosscuda-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or P100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

If using a P100 GPU node, it is advised to request all 32 CPUs there. If running an older version of GROMACS (up to 2021.3) on a K40 node, it is advised to request a low number of CPUs (~ 4), to leave enough CPUs for other GPU jobs to use the other K40 cards on the node.



Sample job submission script sub.sh to run v. 2021.3 and use 16 CPU cores on one node and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --gres=gpu:K40:1 # Request one K40 gpu
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task = 16 # 16 cpus per task
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt $SLURM_CPUS_PER_TASK [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testgromacs''' should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node(--cpus-per-task), a suitable wall time (the example above specifies 4 hours), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-25T18:01:55Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6, 2019.4, 2020, 2020.3, 2021.2, 2021.3, 2021.4

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE) David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-fosscuda-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020.3-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-fosscuda-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.2-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-fosscuda-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.3-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-fosscuda-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.4-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-fosscuda-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or P100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

If using a P100 GPU node, it is advised to request all 32 CPUs there. If running an older version of GROMACS (up to 2021.3) on a K40 node, it is advised to request a low number of CPUs (~ 4), to leave enough CPUs for other GPU jobs to use the other K40 cards on the node.



Sample job submission script sub.sh to run v. 2021.3 and use 16 CPU cores and 4 GPU K40 cards:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --gres=gpu:K40:4 # Request one K40 gpu
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task = 16 # 16 cpus per task
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testgromacs''' should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node(--cpus-per-task), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-25T18:01:01Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6, 2019.4, 2020, 2020.3, 2021.2, 2021.3, 2021.4

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE) David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-fosscuda-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020.3-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-fosscuda-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.2-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-fosscuda-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.3-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-fosscuda-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.4-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-fosscuda-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or p100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

If using a P100 GPU node, it is advised to request all 32 CPUs there. If running an older version of GROMACS (up to 2021.3) on a K40 node, it is advised to request a low number of CPUs (~ 4), to leave enough CPUs for other GPU jobs to use the other K40 cards on the node.



Sample job submission script sub.sh to run v. 2021.3 and use 16 CPU cores and 4 GPU K40 cards:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --gres=gpu:K40:4 # Request one K40 gpu
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task = 16 # 16 cpus per task
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testgromacs''' should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node(--cpus-per-task), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-25T17:58:29Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6, 2019.4, 2020, 2020.3, 2021.2, 2021.3, 2021.4

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE) David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-fosscuda-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020.3-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-fosscuda-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.2-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-fosscuda-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.3-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-fosscuda-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.4-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-fosscuda-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or p100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

If using a P100 GPU node, it is advised to request all 32 CPUs there. If running an older version of GROMACS (up to 2021.3) on a K40 node, it is advised to request a low number of CPUs (~ 4), to leave enough CPUs for other GPU jobs to use the other K40 cards on the node.



Sample job submission script sub.sh to run v. 2021.3 and use 10 CPU cores and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --gres=gpu:K40:1 # Request one K40 gpu
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task = 16 # 16 cpus per task
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testgromacs''' should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node(--cpus-per-task), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-25T15:44:40Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6, 2019.4, 2020, 2020.3, 2021.2, 2021.3, 2021.4

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE)
David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-foss-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020.3-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-foss-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.2-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-foss-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.3-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-foss-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.4-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-foss-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or p100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

If using a P100 GPU node, it is advised to request all 32 CPUs there. If running an older version of GROMACS (up to 2021.3) on a K40 node, it is advised to request a low number of CPUs (~ 4), to leave enough CPUs for other GPU jobs to use the other K40 cards on the node.



Sample job submission script sub.sh to run v. 2021.3 and use 10 CPU cores and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --gres=gpu:K40:1 # Request one K40 gpu
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task = 16 # 16 cpus per task
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testgromacs''' should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node(--cpus-per-task), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-25T15:32:20Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6, 2019.4, 2020, 2020.3, 2021.2, 2021.3, 2021.4

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE)
David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-foss-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020.3-fosscuda-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-foss-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.2-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-foss-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.3-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-foss-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.4-fosscuda-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-foss-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or p100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

If using a P100 GPU node, it is advised to request all 32 CPUs there. If running an older version of GROMACS (up to 2021.3) on a K40 node, it is advised to request a low number of CPUs (~ 4), to leave enough CPUs for other GPU jobs to use the other K40 cards on the node.



Sample job submission script sub.sh to run v. 2021.3 and use 10 CPU cores and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testjob''' should be replaced by a name that is appropriate for your job.
Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-21T20:03:04Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6-gompi-2019b, 2019.4-fosscuda-2019b-PLUMED-2.5.3, 2020-fosscuda-2019b, 2020.3-fosscuda-2019b, 2021.2-fosscuda-2020b, 2021.3-fosscuda-2020b, 2021.4-fosscuda-2020b

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE)
David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-foss-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020.3-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-foss-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.2-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-foss-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.3-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-foss-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.4-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-foss-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or p100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

If using a P100 GPU node, it is advised to request all 32 CPUs there. If running an older version of GROMACS (up to 2021.3) on a K40 node, it is advised to request a low number of CPUs (~ 4), to leave enough CPUs for other GPU jobs to use the other K40 cards on the node.



Sample job submission script sub.sh to run v. 2021.3 and use 10 CPU cores and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt $PBS_NP [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testjob''' should be replaced by a name that is appropriate for your job.
Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-21T15:54:37Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6-gompi-2019b, 2019.4-fosscuda-2019b-PLUMED-2.5.3, 2020-fosscuda-2019b, 2020.3-fosscuda-2019b, 2021.2-fosscuda-2020b, 2021.3-fosscuda-2020b, 2021.4-fosscuda-2020b

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE)
David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-foss-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020.3-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-foss-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.2-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-foss-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.3-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-foss-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.4-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-foss-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or p100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

Sample job submission script sub.sh to run v. 2021.3 and use 10 CPU cores and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-fosscuda-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt $PBS_NP [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testjob''' should be replaced by a name that is appropriate for your job.
Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-21T15:45:28Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6-gompi-2019b, 2019.4-fosscuda-2019b-PLUMED-2.5.3, 2020-fosscuda-2019b, 2020.3-fosscuda-2019b, 2021.2-fosscuda-2020b, 2021.3-fosscuda-2020b, 2021.4-fosscuda-2020b

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE)
David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-foss-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020.3-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-foss-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.2-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-foss-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.3-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-foss-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.4-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-foss-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or p100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

Sample job submission script sub.sh to run v. 2021.3 and use 10 CPU cores and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-foss-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt $PBS_NP [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testjob''' should be replaced by a name that is appropriate for your job.
Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-20T17:13:36Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6-gompi-2019b, 2019.4-fosscuda-2019b-PLUMED-2.5.3, 2020-fosscuda-2019b, 2020.3-fosscuda-2019b, 2021.2-fosscuda-2020b, 2021.3-fosscuda-2020b, 2021.4-fosscuda-2020b

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE)
David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-foss-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020.3-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-foss-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.2-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-foss-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.3-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-foss-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.4-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-foss-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K40, K80 or p100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

Sample job submission script sub.sh to run v. 2021.3 and use 10 CPU cores and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-foss-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt $PBS_NP [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testjob''' should be replaced by a name that is appropriate for your job.
Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-20T16:58:51Z

Keeko:

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6-gompi-2019b, 2019.4-fosscuda-2019b-PLUMED-2.5.3, 2020-fosscuda-2019b, 2020.3-fosscuda-2019b, 2021.2-fosscuda-2020b, 2021.3-fosscuda-2020b, 2021.4-fosscuda-2020b

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE)
David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-foss-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020.3-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-foss-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.2-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-foss-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.3-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-foss-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.4-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-foss-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K20,K40, or p100 GPUs.

Sample job submission script sub.sh to run v. 2021.3 and use 10 CPU cores and 1 GPU K40 card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=testgromacs # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --mem=20gb # Job memory request
#SBATCH --time=4:00:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out # Standard output log
#SBATCH --error=%x.%j.err # Standard error log

module load GROMACS/2021.3-foss-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt $PBS_NP [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testjob''' should be replaced by a name that is appropriate for your job.
Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-20T16:52:49Z

Keeko: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
===Category===
Chemistry
===Program On===
Sapelo2
===Version===
4.5.6-gompi-2019b, 2019.4-fosscuda-2019b-PLUMED-2.5.3, 2020-fosscuda-2019b, 2020.3-fosscuda-2019b, 2021.2-fosscuda-2020b, 2021.3-fosscuda-2020b, 2021.4-fosscuda-2020b

===Author / Distributor===
First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE)
David van der Spoel (Biomedical Centre, Uppsala, SE)
Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)
.

===Description===
GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''Version 4.5.6'''

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/4.5.6-gompi-2019b-PLUMED-2.5.3
</pre>

'''Version 2019.4'''

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3
</pre>

'''Version 2020'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020-foss-2019b
</pre>

'''Version 2020.3'''

This version was compiled with fosscuda-2019b. It is installed in apps/eb/GROMACS/2020.3-foss-2019b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2020.3-foss-2019b
</pre>

'''Version 2021.2'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.2-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.2-foss-2020b

</pre>'''Version 2021.3'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.3-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.3-foss-2020b
</pre>

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

'''Version 2021.4'''

This version was compiled with fosscuda-2020b. It is installed in apps/eb/GROMACS/2021.4-foss-2020b. To use this version of Gromacs, please first load its module with
<pre class="gcommand">
module load GROMACS/2021.4-foss-2020b
</pre>

With the release of version 5.0 of GROMACS, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command<pre class="gcommand">
mdrun --help
</pre>

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following <pre class="gcommand">
source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help
</pre>

All versions of GROMACS except 2021.4 can run with K20,K40, or p100 GPUs.

Sample job submission script sub.sh to run v. 2021.3 and use 10 CPU cores and 1 GPU K40 card:

<pre class="gscript">
#PBS -S /bin/bash
#PBS -q gpu_q
#PBS -N testjob
#PBS -l nodes=1:ppn=10:gpus=1:K40
#PBS -l walltime=4:00:00:00
#PBS -l mem=20gb

cd $PBS_O_WORKDIR

module load GROMACS/2021.3-foss-2020b

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt $PBS_NP [options]

</pre>
where [options] need to be replaced by the arguments you wish to use. The job name '''testjob''' should be replaced by a name that is appropriate for your job.
Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

=== Documentation ===
Please see http://www.gromacs.org/
=== Installation ===

=== System ===
64-bit Linux

GROMACS-Sapelo2

2022-01-20T16:24:24Z

Keeko: /* Running Program */

GROMACS-Sapelo2

2022-01-19T19:26:54Z

Keeko:

GROMACS-Sapelo2

2022-01-19T19:00:36Z

Keeko: formatting

GROMACS-Sapelo2

2022-01-19T18:59:36Z

Keeko: versions available

GROMACS-Sapelo2

2022-01-19T18:58:43Z

Keeko: Created page with "Category:Sapelo2Category:SoftwareCategory:Chemistry ===Category=== Chemistry ===Program On=== Sapelo2 ===Version=== 4.5.6-gompi-2019b,2019.4-fosscuda-2019b-PLUMED-..."

Software

2022-01-19T15:14:23Z

Keeko: added GROMACS

,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-












| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-





| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

































|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-










| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 4.5.6,2019.4,2020,2020.3,2021.2,2021.3,2021.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 3.7.4, 2.7.16 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 3.5.0, 3.6.2, 4.0.0, 4.1.0 || [[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2020.28.61328, 2021.16.61629 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->































| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

































| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

Software

2022-01-19T15:11:41Z

Keeko:

On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-












| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-





| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

































|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-










| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 2016.4, 2018.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 3.7.4, 2.7.16 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 3.5.0, 3.6.2, 4.0.0, 4.1.0 || [[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2020.28.61328, 2021.16.61629 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->































| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

































| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
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[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]