Process `installVEPcache (installVEPcache)` terminated with an error exit status (104)

[rashidma]

I am running nextNEOpi on a ubuntu 22.04.2 LTS running under windows.

NXF_VER=22.10.8 nextflow run /mnt/e/Mamoon/software/nextNEOpi-master/nextNEOpi.nf \
     --batchFile batch_fastq.csv \
     -config /mnt/e/Mamoon/software/nextNEOpi-master/conf/params.config \
     --outputDir testresult \
     --trim_adapters true \
     --trim_adapters_RNAseq true \
     --use_NetChop false \
     -profile singularity \
     -resume \
         --accept_license

singularity 3.11.5 openjdk version "17.0.8.1" 2023-08-24 OpenJDK Runtime Environment (build 17.0.8.1+1-Ubuntu-0ubuntu122.04) OpenJDK 64-Bit Server VM (build 17.0.8.1+1-Ubuntu-0ubuntu122.04, mixed mode, sharing)

I got the below errors:

_[91/43af4b] NOTE: Process installVEPcache (installVEPcache) terminated with an error exit status (104) -- Execution is retried (1) Error executing process > 'installVEPcache (installVEPcache)'

Caused by: Process installVEPcache (installVEPcache) terminated with an error exit status (104)

Command executed:

mkdir -p /mnt/e/Mamoon/db_nextflow/databases/vep_cache vep_install \ -a cf \ -s homo_sapiens \ -y GRCh38 \ -c /mnt/e/Mamoon/db_nextflow/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 /mnt/e/Mamoon/db_nextflow/databases/vep_cache/.homo_sapiens_GRCh38_110_cache_ok.chck

Command exit status: 104

Command output: WARNING: Unable to carry out version check for 'ensembl-vep'

• getting list of available cache files

Command error: WARNING: Unable to carry out version check for 'ensembl-vep'

• getting list of available cache files_

Please let me know what is going wrong?

Thanks a lot

[riederd]

Hi,

The two most common reasons for the VEP version check to fail are:

1) Internet connectivity issues when running the installer 2) Lack of write permissions to the ensembl-vep folder

Does your machine have internet connectivity? Do you have permissions to write to /mnt/e/Mamoon/db_nextflow/databases/vep_cache

[rashidma]

Hello, Yes i have wifi connection but may be under firewall. It might block some links.

Yes. i do have write permissions in the /mnt/e/Mamoon/db_nextflow/databases/vep_cache . I will try to figure it out and let you soon.

Thank you for your time.

[riederd]

I assume it worked now, so I'm closing the issue. Feel free to reopen in case it persists.

[rashidma]

Dear Reider, Yes, vep issue solved. I believe it was due to an internet problem. Thank you.

But, another issue popped up. Now, mkfifo problem, during "mhc_extract" step. Error is something like "mkfifo operation not permitted".

I looked into that and i found this is due to running ubuntu in Windows through WSL2.

Please advise now what to do.

Best regards

Mamoon

On Wed, Nov 15, 2023 at 5:02 PM Dietmar Rieder @.***> wrote:

I assume it worked now, so I'm closing the issue. Feel free to reopen in case it persists.

— Reply to this email directly, view it on GitHub https://github.com/icbi-lab/nextNEOpi/issues/57#issuecomment-1812590994, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE6KEOF63VA6B5OUQO3QY6TYETDQLAVCNFSM6AAAAAA6MEKEDOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJSGU4TAOJZGQ . You are receiving this because you authored the thread.Message ID: @.***>

--

Mamoon Rashid, PhD (Bioinformatics)

Associate Research Scientist

Department of Biostatistics and Bioinformatics

King Abdullah International Medical Research Center (KAIMRC) Kingdom of Saudi Arabia