#333 Assertion `bof->bufferPos <= bof->bufferLen' failed

[Mahul Chakraborty]

After the mhap overlapper stage, I am getting the following error at the overlapStore building step

overlapStoreBuild: AS_OVS_overlapFile.C:185: int AS_OVS_readOverlap(BinaryOverlapFile, OVSoverlap): Assertion `bof->bufferPos <= bof->bufferLen' failed.

Do you know why the assertion might be failing?

[Sergey Koren]

This means one of the overlap job output files is corrupt. Most likely one of the jobs failed to complete or was termintated. You can find which overlaps failed by running:
convertOverlap -a -i <X.ovb*> > /dev/null
echo $?
for each ovb/ovb.gz file in your 1-overlapper/001,002,etc folders.

You can re-run the failed jobs (or re-submit them to the grid). After that, you can resume the pipeline and it should build the overlap store. If this is during correction, you may also need to re-run the step which generates the *.dat files (ovlprep.sh) if you do not have 1-overlapper/*.dat files in your folder.

[Mahul Chakraborty]

Thanks for the suggestion, Sergey.
Yes, this happened during the correction stage.. One of the ovb file (#77)
was corrupted, it seems. I am rerunning the job manually.

On Fri, Dec 4, 2015 at 10:37 AM Sergey Koren skoren@users.sf.net wrote:

This means one of the overlap job output files is corrupt. Most likely one
of the jobs failed to complete or was termintated. You can find which
overlaps failed by running:
convertOverlap -a -i <X.ovb*> > /dev/null
echo $?
for each ovb/ovb.gz file in your 1-overlapper/001,002,etc folders.

You can re-run the failed jobs (or re-submit them to the grid). After
that, you can resume the pipeline and it should build the overlap store. If
this is during correction, you may also need to re-run the step which
generates the .dat files (ovlprep.sh) if you do not have
1-overlapper/.dat files in your folder.

---

• [bugs:#333] http://sourceforge.net/p/wgs-assembler/bugs/333/ Assertion
  `bof->bufferPos <= bof->bufferLen' failed*

Status: open
Group: overlapper
Created: Thu Dec 03, 2015 09:45 AM UTC by Mahul Chakraborty
Last Updated: Thu Dec 03, 2015 09:45 AM UTC
Owner: nobody

After the mhap overlapper stage, I am getting the following error at the
overlapStore building step

overlapStoreBuild: AS_OVS_overlapFile.C:185: int
AS_OVS_readOverlap(BinaryOverlapFile, OVSoverlap): Assertion
`bof->bufferPos <= bof->bufferLen' failed.

Do you know why the assertion might be failing?

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