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Canvas - Copy number variant (CNV) calling from DNA sequencing data
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Germline-WGS fails with binned failed #121

Closed jazberna1 closed 5 years ago

jazberna1 commented 5 years ago

Hello,

I am getting this error when running the Germline-WGS mode of canvas, like this:

dotnet /software/Canvas-1.40.0.1613+master_x64/Canvas.dll Germline-WGS \ --bam /data/HCC1143_T/aligned.sorted.marked_duplicates.bam \ --sample-name HCC1143_T \ --output /ouput/HCC1143_T \ --reference /reference/hs37d5.fa \ --population-b-allele-vcf /reference/1000GENOMES-phase_3.SNV.PASS.header.vcf \ --genome-folder /canvas \ --filter-bed /canvas/filter.bed

The error says:

2019-06-09T17:39:51+02:00,ERROR: Job HCC1143_T_0.binned failed with exit code 137. Job logs: /ouput/HCC1143_T/Logging/HCC1143_T_0.binned.stdout /ouput/HCC1143_T/Logging/HCC1143_T_0.binned.stderr

The file HCC1143_T_0.binned.stdout does not contain any error messages. The file HCC1143_T_0.binned.stderr is empty.

I was wondering if you could please advise me to avoid the error. I am wondering if the error has to do with the chromosome numbering as I don't have a '0' chromosome.

Thanks Jorge

jazberna1 commented 5 years ago

Hi,

I should mention that I got the same error as above with SmallPedigree-WGS instead of Germline-WGS.

Jorgr

eroller commented 5 years ago

The 0 in the file name does not refer to the chromosome name. In the CanvasLog.txt file you should see the subcommand being launched. You can try to run the same command directly on the command line to see what the error is.

jazberna1 commented 5 years ago

Hello Eric,

It was an error on my side.

Thanks so much Jorge