Continuous "core dumped" errors during the M step

[KANGseungseok]

Hello,
I am a student who wants to perform somatic variant calling using CaVEMan.

I am experiencing continuous "core dumped" errors during the M step. While most areas are unaffected, I always encounter a segmentation fault (core dumped) at specific CHR and POS locations for the sample. Even when I retry only those specific locations, the same problem occurs. (I will attach a screenshot of the log file).

If there are any solutions or ways to adjust the memory for this problem, I would appreciate your help.
Thank you very much.

[davidrajones]

Hi there,

The error at the bottom suggests CaVEMan can't see a covariate output file it is expecting to see. How are you running CaVEMan? In the same directory each time? However this may be from the merge step trying to run even though previous M steps have failed.

It looks like you're setting -a 100 in the mstep. This is exceptionally low. What's the coverage at the locations you're seeing issues with? samtools view -c <path/to/bam> <region>

[Ajburdett]

Closing issue due to lack of response