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ebi-pf-team / interproscan

Genome-scale protein function classification
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[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR #307

Closed ewelinarubin closed 1 year ago

ewelinarubin commented 1 year ago

Hi, I am running the Interproscan on a university computer cluster. At some point, I get an error that is pasted in the subject line.

Here is the part of the log file: 

31/01/2023 15:24:32:328 Welcome to InterProScan-5.60-92.0
31/01/2023 15:24:32:330 Running InterProScan v5 in STANDALONE mode... on Linux
31/01/2023 15:24:35:932 RunID: c0712a-s15.ufhpc_20230131_152435779_czi5
31/01/2023 15:24:42:542 Loading file /blue/juliemeyer/ewelinarubin/interproscan/Bacteria-pep.part_001.fasta
31/01/2023 15:24:42:545 Running the following analyses:
[AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2021_04,MobiDBLite-2.0,PANTHER-17.0,Pfam-35.0,PIRSF-3.10,PIRSR-2021_05,PRINTS-42.0,ProSitePatterns-2022_01,ProSiteProfiles-2022_01,SFLD-4,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0]
Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally.
31/01/2023 15:25:16:583 Uploaded 199916 unique sequences for analysis
31/01/2023 15:51:58:280 87% completed
2023-01-31 15:54:40,671 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /blue/juliemeyer/ewelinarubin/interproscan/temp/c0712a-s15.ufhpc_20230131_152435779_czi5//jobFunFam/000000136001_000000140000.raw.out data/gene3d/4.3.0/gene3d_main.hmm /blue/juliemeyer/ewelinarubin/interproscan/temp/c0712a-s15.ufhpc_20230131_152435779_czi5//jobFunFam/000000136001_000000140000.fasta 
Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm.
Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

Can you let me know what I should do? Maybe there is a problem with the installation? are we missing a dependency?

tgrego commented 1 year ago

Hello, you try repressing the modules with python3 setup.py --force interproscan.properties