Closed billzt closed 4 months ago
matthiasblum
commented
3 years ago Hi,
What is printed when running ./interproscan.sh?
Also, does running the following command produce the same error?
./interproscan.sh -appl Pfam -dp -f tsv -goterms -i test_single_protein.fasta
Thank you
billzt
commented
3 years ago Running ./interproscan.sh -appl Pfam -dp -f tsv -goterms -i test_single_protein.fasta has no errors.
Running ./interproscan.sh produces:
(base) [zhutao@log1 interproscan-5.52-86.0]$ ./interproscan.sh
16/09/2021 08:57:59:504 Welcome to InterProScan-5.52-86.0
16/09/2021 08:57:59:508 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).
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.
Coils (2.2.1) : Prediction of coiled coil regions in proteins.
ProSiteProfiles (2021_01) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
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 (2021_01) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
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.
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.
Deactivated analyses:
SignalP_GRAM_POSITIVE (4.1) : Analysis SignalP_GRAM_POSITIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp
Phobius (1.01) : Analysis Phobius is deactivated, because the resources expected at the following paths do not exist: bin/phobius/1.01/phobius.pl
SignalP_EUK (4.1) : Analysis SignalP_EUK is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp
SignalP_GRAM_NEGATIVE (4.1) : Analysis SignalP_GRAM_NEGATIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp
TMHMM (2.0c) : Analysis TMHMM is deactivated, because the resources expected at the following paths do not exist: bin/tmhmm/2.0c/decodeanhmm, data/tmhmm/2.0c/TMHMM2.0c.model
Does it mean that I need to prepare some other components?
KnudNorNielsen
commented
2 years ago Hi, I have the same issue, did you ever solve it?
sdind
commented
10 months ago Hi, I got the same issue and couldn't solve it. Any solution ?
matthiasblum
commented
10 months ago Hi @sdind,
Please paste the full log output. Alternatively, you can use our Docker image.
RUN:
Result