Cheers,
I recently received two independent “errors” from interproscan after running it in two different datasets. Both nucleotides fasta with more than 100k seqs, ran in nucleotide mode. I quoted “errors” because I did not receive actual bug/error report, instead, the jobs finished and the outputs (tsv) were empty; no error message and no std error output (see run info below).
I’ll try run in the other instances (.org, .au) and see if it is a specific .eu problem. In the meantime I hope to get some helpful opinion this.
Thanks!
###tool version
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan5/interproscan/5.0.0
### Command Line
interproscan.sh -dp --input /data/dnb03/galaxy_db/files/a/a/9/dataset_aa95a83b-926e-4ed7-8561-2e33759e001a.dat --seqtype n -f TSV --applications TIGRFAM,PIRSF,ProDom,Panther,SMART,PrositeProfiles,PrositePatterns,HAMAP,PfamA,PRINTS,SuperFamily,Coils,Gene3d,SignalP-EUK,Phobius,TMHMM --tempdir $TEMP --pathways --goterms --iprlookup -o /data/dnb03/galaxy_db/job_working_directory/011/505/11505935/outputs/galaxy_dataset_fa4479c9-10de-42d7-9035-96b0fefa9d68.dat 2>&1
###stdout
/data/dnb03/galaxy_db/job_working_directory/011/505/11505935/working
/opt/galaxy
fooooo
/data/0/interproscan/interproscan-5.36-75.0/
/bin/java
/bin/java
23/09/2020 23:44:14:531 Welcome to InterProScan-5.36-75.0
23/09/2020 23:44:24:260 Running InterProScan v5 in STANDALONE mode... on Linux
23/09/2020 23:44:58:842 Loading file /data/dnb03/galaxy_db/files/a/a/9/dataset_aa95a83b-926e-4ed7-8561-2e33759e001a.dat
23/09/2020 23:44:58:852 Running the following analyses:
[Coils-2.2.1,Gene3D-4.2.0,Hamap-2019_01,PANTHER-14.1,Pfam-32.0,Phobius-1.01,PIRSF-3.02,PRINTS-42.0,ProDom-2006.1,ProSitePatterns-2019_01,ProSiteProfiles-2019_01,SignalP_EUK-4.1,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0,TMHMM-2.0c]
2020-09-24 00:39:26,642 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.business.sequence.NucleotideSequenceLoader:132] WARN - You are analysing more than 2000 nucleotide sequences. Either use an external tool to translate the sequences or Chunk the input and then send the chunks to InterProScan. Refer to https://github.com/ebi-pf-team/interproscan/wiki/ScanNucleicAcidSeqs#improving-performance
24/09/2020 00:47:20:215 Loading file /data/dnb03/galaxy_db/job_working_directory/011/505/11505935/tmp/vgcnbwc-compute-c20me-8483.novalocal_20200923_234424257_c6n2//jobLoadNucleicAcidSequence/orfs.filtered.fasta
24/09/2020 00:47:20:218 Running the following analyses:
[Coils-2.2.1,Gene3D-4.2.0,Hamap-2019_01,PANTHER-14.1,Pfam-32.0,Phobius-1.01,PIRSF-3.02,PRINTS-42.0,ProDom-2006.1,ProSitePatterns-2019_01,ProSiteProfiles-2019_01,SignalP_EUK-4.1,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0,TMHMM-2.0c]
Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete...