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PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool
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Issue with BGZIP, running pharmcat_pipeline on VCF Files #165

Closed JC-Delmas closed 8 months ago

JC-Delmas commented 11 months ago

Hello,

I've encountered an issue when trying to run the pharmcat_pipeline script on a VCF file using PharmCAT version 2.8.3.

PharmCAT version: 2.8.3 Python version: 3.10.13 OS: AlmaLinux

python3 pharmcat_pipeline file.vcf -o test/.

PharmCAT version: 2.8.3

Version: 1.3.2
Usage: bgzip [OPTIONS] [FILE] ...
Options:
   -b, --offset INT        decompress at virtual file pointer (0-based uncompressed offset)
   -c, --stdout            write on standard output, keep original files unchanged
   -d, --decompress        decompress
   -f, --force             overwrite files without asking
   -h, --help              give this help
   -i, --index             compress and create BGZF index
   -I, --index-name FILE   name of BGZF index file [file.gz.gzi]
   -r, --reindex           (re)index compressed file
   -s, --size INT          decompress INT bytes (uncompressed size)
   -@, --threads INT       number of compression threads to use [1]

It appears that the script is not processing the VCF file as expected and instead is returning the usage information for bgzip.

Could you please provide some guidance on how to resolve this issue? Any help or suggestions would be greatly appreciated.

Thank you for your assistance

markwoon commented 11 months ago

It looks like you are running an old version of bgzip.

Bgzip comes from samtools, and we require version 1.18.0.

BinglanLi commented 8 months ago

Closing due to lack of response.