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bedGraphToBigWig sort error #140

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ChrDec opened this issue Apr 28, 2020 · 0 comments
Open

bedGraphToBigWig sort error #140

ChrDec opened this issue Apr 28, 2020 · 0 comments

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@ChrDec
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ChrDec commented Apr 28, 2020

Hi,

I am getting the following error:

2020-04-28T10:42:37+02:00,ERROR: Job bedGraphToBigWig-coverage.bedgraph.1 failed with exit code 255. Job logs:
/ngs-data-sas/dev/bitools/bivip/bivipdecker/canvas_results/CanvasPedigreeCaller/Logging/bedGraphToBigWig-coverage.bedgraph.1.stdout
/ngs-data-sas/dev/bitools/bivip/bivipdecker/canvas_results/CanvasPedigreeCaller/Logging/bedGraphToBigWig-coverage.bedgraph.1.stderr
Job error message:
/ngs-data-sas/dev/bitools/bivip/bivipdecker/canvas_results/VisualizationTempTestSample/coverage.bedgraph is not case-sensitive sorted at line 1692856. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again.
2020-04-28T10:42:37+02:00,ERROR: Exception caught in WorkDoerFactory. Cancelling all jobs. Exception:
One or more errors occurred. (Job bedGraphToBigWig-coverage.bedgraph.1 failed with exit code 255)

I am using dotnet v2.2.207, the latest version of canvas in SmallPedigree-WGS mode and I updated bedGraphToBigWig to v2.8.

Thank you very much for your help.

Kind regards
Chris

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