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.