Error executing process "installVEPcache"

[ryao-mdanderson]

Dear nextNEOpi authors:

After rounds of singularity images pull failures, I put singularity images in /risapps/singularity/repo/nextneopi/1.4.0, with the following images

apps-01.i-med.ac.at-images-singularity-NeoFuse_dev_92712e07.sif.pulling.1700070865761 apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.4.0_f894e892.sif depot.galaxyproject.org-singularity-ensembl-vep-110.0--pl5321h2a3209d_0.img depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img.pulling.1700070238115 depot.galaxyproject.org-singularity-manta-1.6.0--h9ee0642_1.img depot.galaxyproject.org-singularity-multiqc-1.14--pyhdfd78af_0.img depot.galaxyproject.org-singularity-multiqc-1.14--pyhdfd78af_0.img.pulling.1700070222434 depot.galaxyproject.org-singularity-strelka-2.9.10--h9ee0642_1.img

Then set up variable export NXF_SINGULARITY_CACHEDIR="/risapps/singularity/repo/nextneopi/1.4.0"

I attempted to run command $ nextflow run nextNEOpi.nf --batchFile testdata_batchFile_FASTQ.csv --CNVkit false -profile singularity -config conf/params.config --accept_license

-- outputs see lots of process ... also see the following message Error executing process > 'installVEPcache (installVEPcache)'

Caused by: Process installVEPcache (installVEPcache) terminated with an error exit status (110)

Command executed:

mkdir -p /rsrch3/home/itops/ryao/nextNEOpi/reference/nextneopi-1.4.0//databases/vep_cache vep_install \ -a cf \ -s homo_sapiens \ -y GRCh38 \ -c /rsrch3/home/itops/ryao/nextNEOpi/reference/nextneopi-1.4.0//databases/vep_cache \ --CACHE_VERSION 110 \ --CONVERT 2> vep_errors.txt && \ echo "OK" > .homo_sapiens_GRCh38_110_cache_ok.chck && \ cp -f .homo_sapiens_GRCh38_110_cache_ok.chck /rsrch3/home/itops/ryao/nextNEOpi/reference/nextneopi-1.4.0/databases/vep_cache/.homo_sapiens_GRCh38_110_cache_oexecutor > local (104)

[icbi/nextNEOpi] Pipeline Complete! You can find your results in /rsrch3/home/itops/ryao/nextNEOpi/results ...

I did see outputs in /rsrch3/home/itops/ryao/nextNEOpi/results But I don't know how to fix vep_install error message.

Thank you for your suggestion. Rong Yao

[riederd]

Can you post the log file .nextflow.log

[ryao-mdanderson]

nextflow.log Hi @riederd Please see my attached nextflow.log file. Thank you.

[riederd]

And now I'd need

/rsrch3/home/itops/ryao/nextNEOpi/work/05/de5b175ee91ee21cd64c8f7cf9646e/.command.run
/rsrch3/home/itops/ryao/nextNEOpi/work/05/de5b175ee91ee21cd64c8f7cf9646e/.command.err
/rsrch3/home/itops/ryao/nextNEOpi/work/05/de5b175ee91ee21cd64c8f7cf9646e/.command.log
/rsrch3/home/itops/ryao/nextNEOpi/work/05/de5b175ee91ee21cd64c8f7cf9646e/.command.out
/rsrch3/home/itops/ryao/nextNEOpi/work/05/de5b175ee91ee21cd64c8f7cf9646e/vep_errors.txt

Thanks

[ryao-mdanderson]

vep_errors.txt command.out.txt command.log command.err.txt command.run.txt

Here are they - I put postfix .txt in order to allow upload. Thanks!

[riederd]

Hi, looking at the vep_errors.txt it seems your system has connection issues:

ERROR: Could not connect to FTP host ftp.ensembl.org
Connection timed out

Please make sure that your system can connect to ftp.ensembl.org in order to download the cache files.

[ryao-mdanderson]

Thank you for pointing out. I will try and update with you.

[riederd]

No feedback, assuming the issue as solved