DIAMOND-Teaching
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Category
Bioinformatics
Program On
Teaching
Version
1.0
Author / Distributor
Description
"DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data." More details are at DIAMOND
Running Program
The last version is at /usr/local/apps/gb/diamond/1.0
To use this version, please load the module with
ml diamond/1.0
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_BEDTools
#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=diamond.%j.out
#SBATCH --error=diamond.%j.err
cd $SLURM_SUBMIT_DIR
ml diamond/1.0
diamond [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
module load diamond/1.0 diamond help diamond v0.9.19.120 | by Benjamin Buchfink <buchfink@gmail.com> Licensed under the GNU AGPL <https://www.gnu.org/licenses/agpl.txt> Check http://github.com/bbuchfink/diamond for updates. Syntax: diamond COMMAND [OPTIONS] Commands: makedb Build DIAMOND database from a FASTA file blastp Align amino acid query sequences against a protein reference database blastx Align DNA query sequences against a protein reference database view View DIAMOND alignment archive (DAA) formatted file help Produce help message version Display version information getseq Retrieve sequences from a DIAMOND database file dbinfo Print information about a DIAMOND database file General options: --threads (-p) number of CPU threads --db (-d) database file --out (-o) output file --outfmt (-f) output format 0 = BLAST pairwise 5 = BLAST XML 6 = BLAST tabular 100 = DIAMOND alignment archive (DAA) 101 = SAM Value 6 may be followed by a space-separated list of these keywords: qseqid means Query Seq - id qlen means Query sequence length sseqid means Subject Seq - id sallseqid means All subject Seq - id(s), separated by a ';' 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 qframe means Query frame btop means Blast traceback operations(BTOP) staxids means unique Subject Taxonomy ID(s), separated by a ';' (in numerical order) stitle means Subject Title salltitles means All Subject Title(s), separated by a '<>' qcovhsp means Query Coverage Per HSP qtitle means Query title Default: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore --verbose (-v) verbose console output --log enable debug log --quiet disable console output Makedb options: --in input reference file in FASTA format Aligner options: --query (-q) input query file --strand query strands to search (both/minus/plus) --un file for unaligned queries --unal report unaligned queries (0=no, 1=yes) --max-target-seqs (-k) maximum number of target sequences to report alignments for --top report alignments within this percentage range of top alignment score (overrides --max-target-seqs) --range-culling restrict hit culling to overlapping query ranges --compress compression for output files (0=none, 1=gzip) --evalue (-e) maximum e-value to report alignments (default=0.001) --min-score minimum bit score to report alignments (overrides e-value setting) --id minimum identity% to report an alignment --query-cover minimum query cover% to report an alignment --subject-cover minimum subject cover% to report an alignment --sensitive enable sensitive mode (default: fast) --more-sensitive enable more sensitive mode (default: fast) --block-size (-b) sequence block size in billions of letters (default=2.0) --index-chunks (-c) number of chunks for index processing --tmpdir (-t) directory for temporary files --gapopen gap open penalty --gapextend gap extension penalty --frameshift (-F) frame shift penalty (default=disabled) --matrix score matrix for protein alignment (default=BLOSUM62) --custom-matrix file containing custom scoring matrix --lambda lambda parameter for custom matrix --K K parameter for custom matrix --comp-based-stats enable composition based statistics (0/1=default) --masking enable masking of low complexity regions (0/1=default) --query-gencode genetic code to use to translate query (see user manual) --salltitles include full subject titles in DAA file --sallseqid include all subject ids in DAA file --no-self-hits suppress reporting of identical self hits --taxonmap protein accession to taxid mapping file --taxonnodes taxonomy nodes.dmp from NCBI --taxonlist restrict search to list of taxon ids (comma-separated) Advanced options: --algo Seed search algorithm (0=double-indexed/1=query-indexed) --bin number of query bins for seed search --min-orf (-l) ignore translated sequences without an open reading frame of at least this length --freq-sd number of standard deviations for ignoring frequent seeds --id2 minimum number of identities for stage 1 hit --window (-w) window size for local hit search --xdrop (-x) xdrop for ungapped alignment --ungapped-score minimum alignment score to continue local extension --hit-band band for hit verification --hit-score minimum score to keep a tentative alignment --gapped-xdrop (-X) xdrop for gapped alignment in bits --band band for dynamic programming computation --shapes (-s) number of seed shapes (0 = all available) --shape-mask seed shapes --index-mode index mode (0=4x12, 1=16x9) --rank-ratio include subjects within this ratio of last hit (stage 1) --rank-ratio2 include subjects within this ratio of last hit (stage 2) --max-hsps maximum number of HSPs per subject sequence to save for each query --range-cover percentage of query range to be covered for hit culling (default=50) --dbsize effective database size (in letters) --no-auto-append disable auto appending of DAA and DMND file extensions --xml-blord-format Use gnl|BL_ORD_ID| style format in XML output View options: --daa (-a) DIAMOND alignment archive (DAA) file --forwardonly only show alignments of forward strand Getseq options: --seq Sequence numbers to display.
Installation
source code from DIAMONDcp CMakeLists.txt CMakeLists.txt.orig
Compiled for generic CPU by following modification:
sed -i 's/-march=native//g' CMakeLists.txt sed -i 's/-Wno-ignored-attributes //g' CMakeLists.txt
System
64-bit Linux