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ebi-pf-team / interproscan

Genome-scale protein function classification
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error run InterProScan5.63-95 with Singularity Container #341

Closed Liyong-Zhang closed 1 year ago

Liyong-Zhang commented 1 year ago

Hi there,

I am trying to use InterProScan following (https://agbase-docs.readthedocs.io/en/latest/interproscan/using_iprs_cmd.html#running-interproscan-with-singularity-or-apptainer-on-hpc).

After downloading dabaset:

wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.63-95.0/alt/interproscan-data-5.63-95.0.tar.gz
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.63-95.0/alt/interproscan-data-5.63-95.0.tar.gz.md5
md5sum -c interproscan-data-5.63-95.0.tar.gz.md

and pulling docker://agbase/interproscan:5.63-95 with Singluarity, I run with the following command:

singularity run -B ${workdir}:/data -B ${db}:/opt/interproscan/data interproscan_5.63-95.sif -i pep.fa -d $outdir -f tsv,json,xml,gff3 -g -c -p -n biocurator -D database -x 90675 -l > "interproscan_Nov9.log" 2> "interproscan_Nov9.stderr"

The error message is "ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back."

See details at the attached log file: interproscan_Nov9.log

Please help me take a look when you get a chance.

Many thanks, Liyong

matthiasblum commented 1 year ago

Hi @Liyong-Zhang,

Could you give our own Docker image a try? AgBase's image is not official, and seems to have different options, therefore limiting the help we can provide.

Liyong-Zhang commented 1 year ago

Hi Matthias,

Thanks for the suggestion. I have already installed the original interproscan from (https://interproscan-docs.readthedocs.io/en/latest/) and run successfully. I forgot to close this. Sorry for the bother.

Liyong