Failure in starting the annotation process for a hg19 VCF file

[farshadf]

Describe the bug
When a new VCF file is uploaded (created in hg19), the annotation process fails with the following error message:

Upload Failure
This is often caused by improper input files. Check that your input is in a form OpenCRAVAT accepts.

If you think this was caused by an error, [let us know](mailto:support@opencravat.org)

Details: [Errno 2] No such file or directory: '/usr/local/lib/python3.11/site-packages/cravat/conf/cravat.yml

I have checked inside the docker container and this folder exists and is accessible from inside the docker.
I have not tested this process for a VCF file in hg38 genome.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'Jobs/Variants'
2. Click on 'hg38/GRCh38' or "hg19/GRCh37"
3. upload your vcf file
4. Scroll down to 'Annotations' and choose "Genes" or "Variants"
5. Press "Annotate"
6. See error

Expected behavior
To upload the file correctly and start annotating the variants.

Screenshots

Desktop (please complete the following information):

• OS: Windows
• Browser Firefox
• Version: 144

Additional context
OpenCravat is running from a docker container, created using the docker-composer YML script template provided by the developers. This is the content:

version: '3'
services:
  oc-gui:
    image: karchinlab/opencravat:2.17.0
    volumes:
      - '/mnt/test/opencravat/conf:/mnt/conf'
      - '/mnt/test/modules:/mnt/modules'
      - '/mnt/test/jobs:/mnt/jobs'
      - '/mnt/test/logs:/mnt/logs'
    ports:
    - '8081:8080'
    command: ['oc', 'gui']

This is how top of the example VCF file used for this test looks like:

##fileformat=VCFv4.1
##source = mergeVariants {vhgsl}
##FILTER=<ID=g_LowQual,Description="Low quality">
##FORMAT=<ID=g_AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=g_DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=g_GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=g_GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=g_PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##GATKCommandLine=

[kmoad]

Hi @farshadf

This probably isn't an issue with the vcf file itself.

I think there is an underlying issue with how your config files are set up. Are there any files present in /mnt/test/opencravat/conf (/mnt/conf within the container)?