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Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
https://balsamic.readthedocs.io/
MIT License
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[ Failed Analysis ] : Validation case errors on TNhaplotyper #793

Closed ashwini06 closed 3 years ago

ashwini06 commented 3 years ago

Case or sample information Internal sample id or case id: moralgoat, civilsole, fleetjay Amount read-pairs: Sequence type: WGS TN, WGS T-only

Error message Slurm Job_id=1888477 Name=BALSAMIC.moralgoat.bcftools_filter_tnhaplotyper_tumor_normal.48.sh Failed, Run time 00:00:14, FAILED, ExitCode 1

Slurm Job_id=1888368 Name=BALSAMIC.civilsole.bcftools_filter_tnhaplotyper_tumor_only.31.sh Failed, Run time 00:01:19, FAILED, ExitCode 1

Slurm Job_id=1888425 Name=BALSAMIC.fleetjay.bcftools_filter_tnhaplotyper_tumor_normal.48.sh Failed, Run time 00:00:09, FAILED, ExitCode 1

Link to the error message /home/proj/stage/cancer/cases/moralgoat/logs/BALSAMIC.moralgoat.bcftools_filter_tnhaplotyper_tumor_normal.48.sh_1888477.err /home/proj/stage/cancer/cases/civilsole/logs/BALSAMIC.civilsole.bcftools_filter_tnhaplotyper_tumor_only.31.sh_1888368.err

/home/proj/stage/cancer/cases/fleetjay/logs/BALSAMIC.fleetjay.bcftools_filter_tnhaplotyper_tumor_normal.48.sh_1888425.err

Reason for failure

Failed to read from /home/proj/stage/cancer/cases/moralgoat/analysis/vep/SNV.somatic.moralgoat.tnhaplotyper.all.filtered.pass.vcf.gz: No such file or directory
[E::hts_open_format] Failed to open file "/home/proj/stage/cancer/cases/civilsole/analysis/vep/SNV.somatic.civilsole.tnhaplotyper.all.filtered.pass.vcf.gz" : No such file or directory
Failed to read from /home/proj/stage/cancer/cases/civilsole/analysis/vep/SNV.somatic.civilsole.tnhaplotyper.all.filtered.pass.vcf.gz: No such file or directory
Failed to open file "/home/proj/stage/cancer/cases/fleetjay/analysis/vep/SNV.somatic.fleetjay.tnhaplotyper.all.filtered.pass.vcf.gz" : No such file or directory
Failed to read from /home/proj/stage/cancer/cases/fleetjay/analysis/vep/SNV.somatic.fleetjay.tnhaplotyper.all.filtered.pass.vcf.gz: No such file or directory

If workflow, which rules

https://github.com/Clinical-Genomics/BALSAMIC/blob/bc05d40feef0ce321191b192b6ae1053a29b33d5/BALSAMIC/snakemake_rules/annotation/varcaller_wgs_filter_tumor_normal.rule#L75

https://github.com/Clinical-Genomics/BALSAMIC/blob/bc05d40feef0ce321191b192b6ae1053a29b33d5/BALSAMIC/snakemake_rules/annotation/varcaller_wgs_filter_tumor_only.rule#L90

Version (please complete the following information): 8.1.0

ashwini06 commented 3 years ago

Fixed in #794