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Does threading not work nicely with Somatic caller? #149

@cappuchinese

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@cappuchinese

I use LoFreq somatic mode for my pipeline and noticed it was running pretty long in single thread (8hrs). I tried using the --threads option multiple times with different values, but it never seems to work. It always results in the following error:

CRITICAL [2024-12-01 18:31:08,389]: Somatic SNV caller failed. Exiting

I run it with the following command:

lofreq somatic  -n normal.bam -t tumor.bam -f ref.fasta -l regions.bed --call-indels --continue

Is there a reason why this error only pops up when run in multi-threads?
If you need additional info, please let me know

Edit: I also use --continue if I know the normal and tumor files are complete.

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