Dietmar Rieder
Dietmar Rieder
Closing due to inactivity, please feel free to reopen.
Hi, I think we found the root of the issue. We will provide a fix soon, thanks.
Hi, it seems you are missing `HLA_parser.py` which should be in your nextneopi `bin` directory.
Hi, I'm afraid I need more information to track this down. Can you please provide the `first_batchFile_BAM.csv` file and the `.nextflow.log` file?
I tried to reproduce this but I did not run in to the same issue. Which version of the pipeline do you use?
Thanks for reporting and your feedback @mantczakaus and @gilsonmm . I could now reproduce the issue and pushed a fix, please check and let me know if it works.
Hi, There should be nothing that tries to write into the singularity image. The image is read-only anyway. All paths for generating output are bind mounted (-B) into the image....
Can you try to change into `/vf/users/gilsonmm/neoantigen/nextNEOpi/work/6e/fe1289efb29a6006164e375621c8dc` then run `bash .command.run` and monitor the disk space and the files created in that directory and `/vf/users/gilsonmm/neoantigen/nextNEOpi/temporary` as well as `/tmp`
that's bad, I have no idea how I could reproduce this. The error comes from mutect2 (gatk). You might try to run the command in `.command.sh` using a local installation...
Can you try the latest version (1.5.0) and see if you still encounter this issue?