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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Error executing process > 'installVEPcache (installVEPcache)' #7

Closed beijish closed 2 years ago

beijish commented 2 years ago

Good evening,

thank you very much for sharing this tool, very useful. However, I am stuck. I am trying to run it on an HPC (unix, LMOD) system, with these settings: $PBS_O_WORKDIR/nextflow run $PBS_O_WORKDIR/nextNEOpi.nf --batchFile $PBS_O_WORKDIR/batchFile_FASTQ.csv
-profile singularity,cluster
-config $PBS_O_WORKDIR/conf/params.config
--accept_license
--outputDir $PBS_O_WORKDIR/nextNEOpi_results
--tmpDir $PBS_O_WORKDIR/tmp
--HLAHD_DIR $PBS_O_WORKDIR/hlahd.1.5.0
-resume

It starts, and after few hours it terminates with this:

Error executing process > 'installVEPcache (installVEPcache)'

Caused by: Process installVEPcache (installVEPcache) terminated with an error exit status (30)

Command executed:

mkdir -p /xxx/resources/databases/vep_cache vep_install \ -a cf \ -s homo_sapiens \ -y GRCh38 \ -c /xxx/resources/databases/vep_cache \ --CACHE_VERSION 105 \ --CONVERT 2> vep_errors.txt && \ echo "OK" > .homo_sapiens_GRCh38_105_cache_ok.chck && \ cp -f .homo_sapiens_GRCh38_105_cache_ok.chck /mnt/panfs1/scratch/wsspaces/svalpione-Kim2018-0/WES/resources/databases/vep_cache/.homo_sapiens_GRCh38_105_cache_ok.chck

Command exit status: 30

Command output: curl failed (000), trying to fetch using LWP::Simple LWP::Simple failed (500), trying to fetch using HTTP::Tiny

Command wrapper: curl failed (000), trying to fetch using LWP::Simple LWP::Simple failed (500), trying to fetch using HTTP::Tiny

Work dir: /xxx/work/cc/81435e84c23743ca08bca184d1ce9c

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

I the server is connected to Internet, I have tried to install VEP and populate vep_cache prior to launching the job but it makes no difference. Any suggestions, please?

Thank you a lot

S

riederd commented 2 years ago

Hi, thanks for your interest in nextNEOpi.

To me this looks like a temporary connection/server issue. Seen that you installed the vep_cache manually, you may try the following:

$ echo OK > /mnt/panfs1/scratch/wsspaces/svalpione-Kim2018-0/WES/resources/databases/vep_cache/.homo_sapiens_GRCh38_105_cache_ok.chck

And then resume the pipeline. All assuming that you successfully installed the vep_cache in /mnt/panfs1/scratch/wsspaces/svalpione-Kim2018-0/WES/resources/databases/vep_cache/

riederd commented 2 years ago

No feedback, assuming that the issue is fixed. Closing it for now, feel free to reopen.

beijish commented 2 years ago

Hi, it worked installing manually. There is a problem with certificates that prevents the connections called by vep_install. I have been able to bypass most of these skipping the certificate check for most curl/wget commands in the nextNEOpi pipeline. You might want to look into this for the next releases? Thanks

SV

riederd commented 2 years ago

...hm I tried to reproduce your issue, however I do not get any error. I tested:

beijish commented 2 years ago

Thank you, it turned out there was a problem with certificates with our nodes. Help much appreciated.

SV

riederd commented 2 years ago

Glad you found the problem