Data bundle update error

[xgnusr]

Hello:

• [pcgr 1.4.1.9016] Version of PCGR.
• [grch38 ] Genome build
• the complete command you used to invoke pcgr (including all explicit options):

pcgr --input_vcf final_output.vcf.gz \ --vep_dir /home/xgnusr/pcgr \ --refdata_dir /home/xgnusr/pcgr \ --output_dir out_pcgr_0119062024/ \ --genome_assembly grch38 \ --sample_id TEST01 \ --tumor_purity 0.9 \ --vep_n_forks 8 \ --vep_buffer_size 1024 \ --estimate_tmb \ --estimate_signatures \ --tumor_site 0 \ --assay WGS

• the full error message:

2024-06-19 10:07:33 - pcgr-check-files - ERROR - 2024-06-19 10:07:33 - pcgr-check-files - ERROR - The PCGR data bundle is not compliant with the software version - please download the latest software and data bundle (see https://github.com/sigven/cpsr for instructions) 2024-06-19 10:07:33 - pcgr-check-files - ERROR -

The error occurred when updating the data contained in:

pcgr_ref_data.20240612.grch38.tgz and homo_sapiens_vep_112_GRCh38.tar.gz

TNX !!

[sigven]

Hi @xgnusr ,

Thanks for your feedback! The version you have tested is still not yet available as an official release, we are still working on pushing it for our new release. That being said, I am curious about your error using the development version. Could you indicate:

1) Whether you use Conda or Docker for running PCGR? 2) What is indicated when you type the follwing on the command-line: cat /home/xgnusr/pcgr/data/grch38/.PCGR_BUNDLE_VERSION ?

best, Sigve

[xgnusr]

Hi Sigven,

PCGR is the best application for oncologists that exists. Thank you very much for this great contribution to cancer researchers.

Indeed the discrepancy was in that file, once they match everything works perfectly.

I currently use 'apptainer' but prefer the conda environment.

Version 1.4.1 has been the best so far, more complete from my point of view.

Sorry for the English and again, thank you very much