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cancerit / CaVEMan

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
http://cancerit.github.io/CaVEMan
GNU Affero General Public License v3.0
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1.13.5 - Segmentation fault (core dumped) - Estep #83

Closed ghost closed 5 years ago

ghost commented 6 years ago

As per sections 1 and 2 of the following comment on issue #82

  1. I tried out the pre-release 1.13.5 and I got the Segmentation fault (core dumped) Error message that we all fear :-( I used the exact same inputs and commands I used with version 1.13.2 and 1.13.3.

  2. I tried first using only contigs representing chromosome 21 and 22 as test and got the segmentation fault. Here I attach a zip file with logs and file and commands for that run. Hope it helps.

CaVEMan.run.zip

Reported by @ChristopheLegendre

ghost commented 5 years ago

@ChristopheLegendre I believe this estep problem is due to a missing commandline parameter. Can you add assembly as well as species please? I'll create a new issue to make the checking for these more robust.

Let me know if this works.