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isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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Segmentation fault #47

Closed wzylin closed 7 years ago

wzylin commented 7 years ago

Hi, Graphmap would sometimes be terminated before finished. I dont know what was going on there. Could you help to check? Thank you!

error message .... .... 1 (35.33%) [m: 38765, u: 4570], length = 4567, qname: d2055667-23e2-4a2f-9f31-15[22:09:37 ProcessReads] [CPU time: 16923.34 sec, RSS: 3080 MB] Read: 43355/122701 (35.33%) [m: 38774, u: 4570], length = 15346, qname: d8bdb47f-cc9a-4769-b9bb-1.../var/spool/torque/mom_priv/jobs/487788.statgenpro.SC: line 10: 11686 Segmentation fault (core dumped) graphmap align -t 12 -r C.elegans_ref.fasta -d allreads_ac.correctedReads.fasta.gz -o all_ac2w.sam

mdcao commented 7 years ago

I ran into the same problem too.

isovic commented 7 years ago

Hi wzylin, I would very much like to inspect this in detail, could you by any chance share the read which causes this?

You can try re-running the process in one thread with -t 1, in this case when program segfaults the qname shown in terminal will be the last one that was supposed to have been processed but failed. Could you extract this read into a separate file, and try mapping only this read to check whether it breaks as expected. If it does, could you send it to me for further inspection?

Thank you, Best regards, Ivan.

isovic commented 7 years ago

Also, which commit are you using?

Ivan

wzylin commented 7 years ago

this problem seems solved when I update the graphmap to 0.3.2. Will let you know when the problem comes up again.