InterProScan-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
5.44-90.0, 5.51-85.0
Author / Distributor
To cite:
Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise Daugherty, Lauranne Duquenne, Robert D. Finn, Julian Gough, Daniel Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Aurélie Laugraud, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Nicola Mulder, Darren Natale, Christine Orengo, Antony F. Quinn, Jeremy D. Selengut, Christian J. A. Sigrist, Manjula Thimma, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, and Corin Yeats (2009) InterPro: the integrative protein signature database
Nucleic Acids Res. 37 (Database Issue):D211-D215.
Description
"InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem." More details are at EMBL-EBI.
Running Program
Also refer to Running Jobs on Sapelo2
For more information on Environment Modules on Sapelo2 please see the Lmod page.
- Version 5.44-90.0, installed in /apps/eb/InterProScan/5.44-79.0-foss-2019b
- panther data 14.1, installed in /apps/eb/InterProScan/5.44-79.0-foss-2019b/data/panther/14.1
- Version 5.51-85.0, installed in /apps/eb/InterProScan/5.51-85.0-foss-2019b
- panther data 15.0, installed in /apps/eb/InterProScan/5.51-85.0-foss-2019b/data/panther/15.0
To use version 5.44-90.0, please first load the module with
module load InterProScan/5.44-79.0-foss-2019b
To use version 5.51-85.0, please first load the module with
module load InterProScan/5.51-85.0-foss-2019b
Please use full paths to your files in your working folder; Otherwise, InterProScan will try to access and write to /app/eb. This will cause IO permission error.
Sample job submission script (sub.sh) to run interproscan.sh of version 5.51-85.0 in a batch job:
#!/bin/bash #SBATCH --job-name=job_InterProScan #SBATCH --partition=batch #SBATCH --ntasks=1 #SBATCH --cpus-per-task=4 #SBATCH --mem=20gb #SBATCH --time=120:00:00 #SBATCH --output=log.%j.out #SBATCH --error=log.%j.err #SBATCH --mail-user=username@uga.edu #SBATCH --mail-type=ALL cd $SLURM_SUBMIT_DIR module load InterProScan/5.51-85.0-foss-2019b sh interproscan.sh [options]
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 cores per node, and the job name need to be modified appropriately as well.
Please do not use the -cpu option, as this option appears to cause some issues on the cluster. You can use the queueing system option ppn to request more than one core within a single node and the application will be able to use those cores. You can also use the -dp option to disable the use of the precalculated match lookup service.
Example of job submission
sbacth sub.sh
Please NOTE: InterProScan5 cluster mode works only for LSF or SGE queueing system InterProScan Cluster Mode. It doesn't work with MOAB queuing system of Sapelo2 cluster.
Documentation
User guide is available at InterProScan Wiki
For help on command line:
ml InterProScan/5.51-85.0-foss-2019b
sh interproscan.sh
23/04/2021 10:38:27:539 Welcome to InterProScan-5.51-85.0
23/04/2021 10:38:27:542 Running InterProScan v5 in STANDALONE mode... on Linux
usage: java -XX:+UseParallelGC -XX:ParallelGCThreads=2 -XX:+AggressiveOpts -XX:+UseFastAccessorMethods -Xms128M
-Xmx2048M -jar interproscan-5.jar
Please give us your feedback by sending an email to
interhelp@ebi.ac.uk
-appl,--applications <ANALYSES> Optional, comma separated list of analyses. If this option
is not set, ALL analyses will be run.
-b,--output-file-base <OUTPUT-FILE-BASE> Optional, base output filename (relative or absolute path).
Note that this option, the --output-dir (-d) option and the
--outfile (-o) option are mutually exclusive. The
appropriate file extension for the output format(s) will be
appended automatically. By default the input file path/name
will be used.
-cpu,--cpu <CPU> Optional, number of cores for inteproscan.
-d,--output-dir <OUTPUT-DIR> Optional, output directory. Note that this option, the
--outfile (-o) option and the --output-file-base (-b) option
are mutually exclusive. The output filename(s) are the same
as the input filename, with the appropriate file extension(s)
for the output format(s) appended automatically .
-dp,--disable-precalc Optional. Disables use of the precalculated match lookup
service. All match calculations will be run locally.
-dra,--disable-residue-annot Optional, excludes sites from the XML, JSON output
-etra,--enable-tsv-residue-annot Optional, includes sites in TSV output
-exclappl,--excl-applications <EXC-ANALYSES> Optional, comma separated list of analyses you want to
exclude.
-f,--formats <OUTPUT-FORMATS> Optional, case-insensitive, comma separated list of output
formats. Supported formats are TSV, XML, JSON, GFF3, HTML and
SVG. Default for protein sequences are TSV, XML and GFF3, or
for nucleotide sequences GFF3 and XML.
-goterms,--goterms Optional, switch on lookup of corresponding Gene Ontology
annotation (IMPLIES -iprlookup option)
-help,--help Optional, display help information
-i,--input <INPUT-FILE-PATH> Optional, path to fasta file that should be loaded on Master
startup. Alternatively, in CONVERT mode, the InterProScan 5
XML file to convert.
-incldepappl,--incl-dep-applications <INC-DEP-ANALYSES> Optional, comma separated list of deprecated analyses that
you want included. If this option is not set, deprecated
analyses will not run.
-iprlookup,--iprlookup Also include lookup of corresponding InterPro annotation in
the TSV and GFF3 output formats.
-ms,--minsize <MINIMUM-SIZE> Optional, minimum nucleotide size of ORF to report. Will only
be considered if n is specified as a sequence type. Please be
aware of the fact that if you specify a too short value it
might be that the analysis takes a very long time!
-o,--outfile <EXPLICIT_OUTPUT_FILENAME> Optional explicit output file name (relative or absolute
path). Note that this option, the --output-dir (-d) option
and the --output-file-base (-b) option are mutually
exclusive. If this option is given, you MUST specify a single
output format using the -f option. The output file name will
not be modified. Note that specifying an output file name
using this option OVERWRITES ANY EXISTING FILE.
-pa,--pathways Optional, switch on lookup of corresponding Pathway
annotation (IMPLIES -iprlookup option)
-t,--seqtype <SEQUENCE-TYPE> Optional, the type of the input sequences (dna/rna (n) or
protein (p)). The default sequence type is protein.
-T,--tempdir <TEMP-DIR> Optional, specify temporary file directory (relative or
absolute path). The default location is temp/.
-verbose,--verbose Optional, display more verbose log output
-version,--version Optional, display version number
-vl,--verbose-level <VERBOSE-LEVEL> Optional, display verbose log output at level specified.
-vtsv,--output-tsv-version Optional, includes a TSV version file along with any TSV
output (when TSV output requested)
Copyright © EMBL European Bioinformatics Institute, Hinxton, Cambridge, UK. (http://www.ebi.ac.uk) The InterProScan
software itself is provided under the Apache License, Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0.html).
Third party components (e.g. member database binaries and models) are subject to separate licensing - please see the
individual member database websites for details.
Available analyses:
TIGRFAM (15.0) : TIGRFAMs are protein families based on hidden Markov models (HMMs).
SFLD (4) : SFLD is a database of protein families based on hidden Markov models (HMMs).
Phobius (1.01) : A combined transmembrane topology and signal peptide predictor.
SignalP_GRAM_NEGATIVE (4.1) : SignalP (gram-negative) predicts the presence and location of signal peptide cleavage sites in amino acid sequences for gram-negative prokaryotes.
SUPERFAMILY (1.75) : SUPERFAMILY is a database of structural and functional annotations for all proteins and genomes.
PANTHER (15.0) : The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
Gene3D (4.3.0) : Structural assignment for whole genes and genomes using the CATH domain structure database.
Hamap (2020_05) : High-quality Automated and Manual Annotation of Microbial Proteomes.
ProSiteProfiles (2019_11) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Coils (2.2.1) : Prediction of coiled coil regions in proteins.
SMART (7.1) : SMART allows the identification and analysis of domain architectures based on hidden Markov models (HMMs).
CDD (3.18) : CDD predicts protein domains and families based on a collection of well-annotated multiple sequence alignment models.
PRINTS (42.0) : A compendium of protein fingerprints - a fingerprint is a group of conserved motifs used to characterise a protein family.
PIRSR (2021_02) : PIRSR is a database of protein families based on hidden Markov models (HMMs) and Site Rules.
ProSitePatterns (2019_11) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
SignalP_EUK (4.1) : SignalP (eukaryotes) predicts the presence and location of signal peptide cleavage sites in amino acid sequences for eukaryotes.
Pfam (33.1) : A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
MobiDBLite (2.0) : Prediction of intrinsically disordered regions in proteins.
SignalP_GRAM_POSITIVE (4.1) : SignalP (gram-positive) predicts the presence and location of signal peptide cleavage sites in amino acid sequences for gram-positive prokaryotes.
PIRSF (3.10) : The PIRSF concept is used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.
TMHMM (2.0c) : Prediction of transmembrane helices in proteins.
Installation
Tarball was downloaded from http://www.ebi.ac.uk/interpro/download/
System
64-bit Linux