Issue with BGZIP, running pharmcat_pipeline on VCF Files
JC-Delmas opened this issue · 2 comments
JC-Delmas commented
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
It looks like you are running an old version of bgzip.
Bgzip comes from samtools, and we require version 1.18.0.
BinglanLi commented
Closing due to lack of response.