Running InterProScan¶
Once you have uncompressed your Obtaining a copy of InterProScan, you can run InterProScan directly from the command line.
Run the supplied shell script. If you run this script with no arguments, you will be presented with the usage instructions:
./interproscan.sh
After a short delay, you will see the following usage instructions:
Welcome to InterProScan-5.57-90.0
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, and GFF3.
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 (XX.X) : TIGRFAMs are protein families based on hidden Markov models (HMMs).
SFLD (X) : SFLD is a database of protein families based on hidden Markov models (HMMs).
SUPERFAMILY (X.XX) : SUPERFAMILY is a database of structural and functional annotations for all proteins and genomes.
PANTHER (XX.X) : 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 (X.X.X) : Structural assignment for whole genes and genomes using the CATH domain structure database.
Hamap (XXXX_XX) : High-quality Automated and Manual Annotation of Microbial Proteomes.
ProSiteProfiles (XXX_XX) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Coils (X.X.X) : Prediction of coiled coil regions in proteins.
SMART (X.X) : SMART allows the identification and analysis of domain architectures based on hidden Markov models (HMMs).
CDD (X.XX) : CDD predicts protein domains and families based on a collection of well-annotated multiple sequence alignment models.
PRINTS (XX.X) : A compendium of protein fingerprints - a fingerprint is a group of conserved motifs used to characterise a protein family.
PIRSR (XXXX_XX) : PIRSR is a database of protein families based on hidden Markov models (HMMs) and Site Rules.
ProSitePatterns (XXXX_XX) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
AntiFam (X.X) : AntiFam is a resource of profile-HMMs designed to identify spurious protein predictions.
Pfam (XX.X) : A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
MobiDBLite (X.X) : Prediction of intrinsically disordered regions in proteins.
PIRSF (X.XX) : 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.
Deactivated analyses:
SignalP_EUK (X.X) : Analysis SignalP_EUK-X.X is deactivated, because the following parameters are not set in the interproscan.properties file: binary.signalp.X.X.path
SignalP_GRAM_NEGATIVE (X.X) : Analysis SignalP_GRAM_NEGATIVE-X.X is deactivated, because the following parameters are not set in the interproscan.properties file: binary.signalp.X.X.path
SignalP_GRAM_POSITIVE (X.X) : Analysis SignalP_GRAM_POSITIVE-X.X is deactivated, because the following parameters are not set in the interproscan.properties file: binary.signalp.X.X.path
Phobius (X.XX) : Analysis Phobius-X.XX is deactivated, because the following parameters are not set in the interproscan.properties file: binary.phobius.pl.path.X.XX
TMHMM (X.X) : Analysis TMHMM-X.Xc is deactivated, because the following parameters are not set in the interproscan.properties file: binary.tmhmm.path, tmhmm.model.path
SignalP_GRAM_NEGATIVE (X.X) : Analysis SignalP_GRAM_NEGATIVE-X.X is deactivated, because the following parameters are not set in the interproscan.properties file: binary.signalp.X.X.path
The latest analysis versions can be obtained by running the InterProScan script without any options specified.
InterProScan test run¶
This distribution of InterProScan provides a set of protein test sequences, which you can use to check how InterProScan behaves on your system. First, if you have not yet run the initialisation script run the following command:
python3 setup.py -f interproscan.properties
This command will press and index the hmm models to prepare them into a format used by hmmscan. This command need only be run once.
You can then run the following two test case commands:
./interproscan.sh -i test_all_appl.fasta -f tsv -dp
./interproscan.sh -i test_all_appl.fasta -f tsv
The first test should create an output file with the default file name test_all_appl.fasta.tsv, and the second would then create test_all_appl.fasta_1.tsv (since the default filename already exists).
Both the above test commands should be run successfully, before running InterProScan on you own input set of sequences.
What should you get?
InterProScan should run through properly without any warnings and it will create a TSV output file containing several member database matches, including Gene3d, PIRSF etc.
The member database binaries supplied with InterProScan should run on most Linux systems, however if they don’t work on a particular system then see the FAQ page, What should I do if one of the binaries included with InterProScan 5 doesn’t work on my system?.
Command-line options¶
-dp / –disable-precalc (optional)¶
InterProScan is a computationally expensive program, sometimes taking a couple of minutes to characterise a single sequence. It calculates matches to InterPro signatures based purely on the amino acid sequence that is submitted to it. Therefore, 2 identical amino acid sequences will produce identical outputs (although if the sequences differ by just one residue, the outputs may or may not be the same). We can take advantage of this feature, and increase the speed of InterProScan, by pre-calculating matches for sequences already found in UniProtKB. When a sequence is submitted to it, InterProScan calculates an MD5 checksum for the amino acid sequence and then uses that checksum to check the What is the InterProScan 5 Lookup Service? pre-calculated lookup service to see whether it has already been encountered. If it has, the pre-calculated results are returned to the user; if not, the InterProScan search algorithms are run against the sequence.
By default, InterProScan has this option turned on. If you wish to turn it off, you should add the “–disable-precalc” option to the command line. Users also have the option of using an EBI-hosted instance of the look-up service (this is what is enabled by default) or downloading a copy and running it locally. For more information, read the section on configuring the match lookup service below
-appl / –applications application_name (optional)¶
By default, all available analyses are run, however if you wish to restrict to a single analysis, use the -appl option. The argument to the -appl option should be one of the analyses named at the bottom of the usage instructions. Analysis names may or may not contain version numbers. For example:
./interproscan.sh -appl Pfam -i /path/to/sequences.fasta
If you wish to specifically run two or more analyses you can include multiple -appl arguments:
./interproscan.sh -appl Pfam-33.1 -appl PRINTS-42.0 -i /path/to/sequences.fasta
or you can use a single -appl option with a comma-separated list of analyses:
./interproscan.sh -appl CDD,COILS,Gene3D,HAMAP,MobiDBLite,PANTHER,Pfam,PIRSF,PRINTS,PROSITEPATTERNS,PROSITEPROFILES,SFLD,SMART,SUPERFAMILY,TIGRFAM -i /path/to/sequences.fasta
A list of all available analyses is in the section “Included Analyses”
-i / –fasta sequence_file¶
To analyse the contents of a fasta file, you should add one argument as in the following example:
./interproscan.sh -i /path/to/sequences.fasta
This will return results in the default formats as described above, i.e., for protein sequences, return TSV, XML and GFF3 files or for nucleotide sequences, return GFF3 and XML files with file names based upon the name of the fasta file. (sequences.tsv, sequence.xml, sequences.gff3 in this case).
-iprlookup,–iprlookup¶
Option that provides mappings from matched member database signatures to the InterPro entries that they are integrated into. Starting from release of InterProScan-5.40-77.0, you don’t have to explicity specify this option
as InterProScan will always provide mappings to InterPro entries.
-goterms,–goterms (optional)¶
Option that provides mappings to the Gene Ontology (GO). These mappings are based on the matched manually curated InterPro entries. (IMPLIES -iprlookup option)
-b / –output-file-base file_name (optional)¶
Optionally, you can supply a path and base name (excluding a file extension) for the results file as follows:
./interproscan.sh -i /path/to/sequences.fasta -b /path/to/output_file
The appropriate file extension will be added to each output file, depending upon the format(s) requested. (It is therefore recommended that you do not include a file extension yourself.)
Note that using this option will not overwrite existing files. If a file with the required name exists at the path specified, the provided file name will have ‘underscore_number’ appended in front of the file extension.
-o / –outfile (optional)¶
This command can be given instead of the -b option. If you provide this argument, you must specify a single output format. The output file will be given the name specified by this option.
Note that this option will overwrite existing files with the same path / name.
-pa / –pathways (optional)¶
Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (IMPLIES -iprlookup option). The different pathways databases that InterProScan provides cross links to are:
MetaCyc
Reactome
-t / –seqtype (optional)¶
InterProScan supports analysis of both protein and nucleic acid sequences (DNA/RNA). Your input sequences are interpreted as protein sequences by default. If you like to scan nucleotide sequences you must set the -t option:
./interproscan.sh -t n -i /path/to/sequences.fasta
-T / –tempdir (optional)¶
Optionally, you can specify the location of the InterProScan temporary directory. This directory is used as a working directory. The default temporary directory will be in the same directory as the InterProScan script file (interproscan.sh). By default, this directory is completely cleaned up after InterProScan finished all analyses successfully.
Example usage:
./interproscan.sh -T /path/to/temp-directory -i /path/to/sequences.fasta
-dra / –disable-residue-annot (optional)¶
Optionally, you can prevent InterProScan from calculating the residue level annotations and displaying in the output where available. If you don’t require this information then disabling the feature will improve performance and result in smaller output files.
-version / –version (optional)¶
Display the version number of the InterProScan software you are running.
Included analyses¶
This distribution of InterProScan includes:
PROSITE (Profiles and Patterns)
SMART (unlicensed components only by default - this analysis has simplified post-processing that includes an E-value filter, however you should not expect it to give the same match output as the fully licensed version of SMART)
A number of other analyses are available in InterProScan. These analyses use licensed code and data provided by third parties. If you wish to run these analyses it will be necessary for you to obtain a licence from the vendor and configure your local InterProScan installation to use these:
The InterPro team would like to thank the developers and maintainers of all of these analyses for their valued and on-going support.
Output format¶
Please see Output formats.
Optional configuration¶
Working directory for temporary files¶
There is a second way of changing temporary/working directory beyond the -T option (where fasta files, binary output etc. are written to). You can do this by editing the interproscan.properties file and change the path for the property:
temporary.file.directory=temp/[UNIQUE]
NOTE: Leave /[!UNIQUE] on the end - this is replaced with a timestamped / unique directory for each run. This directory is cleaned up and deleted at the end of each run of InterProScan.
Configuring the Pre-calculated Match Lookup Service¶
As this is a web service, your servers will need to have external access to http://www.ebi.ac.uk to use it. If you are behind a firewall that prevents such access and you are unable to configure access, you can either turn off use of this service or download a copy and run a local match lookup service.
To turn off use of the service, either use the -dp command line option,
or edit interproscan.properties and comment out* or delete the
following line, near the bottom of the file:
precalculated.match.lookup.service.url=http://www.ebi.ac.uk/interpro/match-lookup
``*``(To comment the line out, add a # to the start of the line.)
Running InterProScan on an LSF/SGE Cluster¶
Please see Cluster Mode.