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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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bgzip error #3639

Closed gis-nlsim closed 2 years ago

gis-nlsim commented 2 years ago

I am running mutation calling and HLA with optitype (separatily), and I'm encountering the same error involving bgzf

Error: unhandled exception: invalid bgzf file [ValueError] hla.config.yaml.txt

# HLA genotyping
---
details:
- algorithm:
    platform: illumina
    quality_format: standard
    aligner: bwa
    save_diskspace: true
    hlacaller: optitype
  analysis: variant2
  resources:
    gatk:
      jvm_opts:
      - -Xms500m
      - -Xmx8g  
  description: TCGA-LN-A49U-H-N
  files: [/scratch/users/astar/gis/simngl/bcbioruns/TCGA-ESCA/bams/BATCH01/288a2fed-c644-49cb-a064-e4f4d14eb664/3d7ac912c7f1a18e7ca131bcc08fa3fc_gdc_realn.bam]
  genome_build: hg38
  metadata:
    batch: TCGA-LN-A49U-H
    phenotype: normal
- algorithm:
    platform: illumina
    quality_format: standard
    aligner: bwa
    save_diskspace: true
    hlacaller: optitype
  analysis: variant2
  description: TCGA-LN-A49U-H-T
  files: [/scratch/users/astar/gis/simngl/bcbioruns/TCGA-ESCA/bams/BATCH01/3b9319c1-307d-48d7-a49d-921c66e77bf4/c226f9156a8b9310d47d9b26d703c576_gdc_realn.bam]
  genome_build: hg38
  metadata:
    batch: TCGA-LN-A49U-H
    phenotype: tumor
fc_date: '2015-07-31'
fc_name: TCGA-LN-A49U-H
upload:
  dir: ../bcbio_final

Seek your assistance in resolving this issue; I am attaching my yaml files, as well as the last 200 lines of the log file.

Thank you.

wxs.config.yaml.txt wxs.error.txt hla.error.txt hla.config.yaml.txt

naumenko-sa commented 2 years ago

Hi @gis-nlsim !

What is your bcbio version?

I think this bug has been fixed in 1.2.9: https://github.com/bcbio/bcbio-nextgen/blob/1d065fe60272b87a687d14eb45aeaf88614b059f/bcbio/qc/viral.py#L46

Sergey

gis-nlsim commented 2 years ago

bash-4.4$ cd /scratch/users/astar/gis/simngl/bcbioruns bash-4.4$ bcbio_nextgen.py --version 1.2.9a

naumenko-sa commented 2 years ago

right, 1.2.9a (alpha) < 1.2.9.

Could you please upgrade to 1.2.9+ ?

bcbio_nextgen.py upgrade -u development

gis-nlsim commented 2 years ago

Sorry, I meant v1.2.9a

bash-4.4$ bcbio_nextgen.py --version 1.2.9a bash-4.4$

naumenko-sa commented 2 years ago

Right, your version 1.2.9a is lesser than v1.2.9, you need to update, versions go

1.2.8, 1.2.9a, 1.2.9 https://github.com/bcbio/bcbio-nextgen/commit/a2cbdd17a2246429976ae0f0b04b84c8b0252049

gis-nlsim commented 2 years ago

Thanks, I’ll try the upgrade.

Sim Ngak Leng Senior Bioinformatics Specialist Computational & Systems Biology 3