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Published 20 hours ago • verified publisher icon walaj

free() error

Open willhooper opened this issue 3 years ago • 3 comments

Hi,

I'm encountering the following error. Svaba runs as normal for a few minutes (judging from the logs), then I get the following error:

--- Loaded non-read data. Starting detection pipeline *** Error in `/nfs/sw/svaba/svaba-0.2.1/svaba': free(): invalid next size (fast): 0x00007f47197bc020 ***

Have you seen this before?

willhooper avatar Nov 04 '20 20:11 willhooper

Hmm, I have not -- is it specific to just a one BAM file or re-creatable on different BAMs?

walaj avatar Nov 05 '20 16:11 walaj

It's happening on several tumor/normal pairs of BAMs that are 2x100bp instead of our usual 2x150bp. Do you think this could be related to the shorter read length?

willhooper avatar Nov 10 '20 19:11 willhooper

Wouldn't matter the size of the reads. It's running into some read that it's not expecting. Does this BAM crash with any other programs? Has it been sorted and indexed by samtools (I assume yes)? Is the reference genome supplied the same as the genome it was aligned to? Sorry wish I could help more, I just don't have much to go off of here.

walaj avatar Nov 12 '20 00:11 walaj