[wgs-assembler-users] Fwd: PBcR error on overlapStoreBuild step

[Santiago R. <san...@gm...>]

Dear CA community,

I'm running the correction of some PacBio reads with high-identity Illumina
reads, in a high memory server, for a 750 Mbp genome. I've considered the
known issues addressed in the website when starting the correction.

When executing the pipeline, I've reached to the overlapStoreBuild step
with 48 ovb files, size 26 Gb each (totaling 1.2Tb). ovls files have
already been deleted by the script. The error happened while executing
overlapStoreBuild:

...
bucketizing DONE!
overlaps skipped:
               0 OBT - low quality
               0 DUP - non-duplicate overlap
               0 DUP - different library
               0 DUP - dedup not requested
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc

Failed with 'Aborted'
...


I ran this step twice: the first one having set ovlStoreMemory to 8192 Mb,
but the second one, set it on 160000 (160 Gb). In the "Overlap store
failure" FAQ, it mentioned as possible causes "Out of disk space" (which is
not my case) and "Corrupt gzip files / too many fragments". I don't have
gzip files and I have only 15 fragments. Also, bucketizing step finishes OK.

Also, some odd thing I've noticed (at least odd for me) is that 14 of the
15 temp files (tmp.sort.XXX) of the asm.ovlStore.BUILDING folder have a
size 79Gb while the last one size is 1.2Tb.

Could anybody tell me what could be the cause of this error and how to
solve it?

I'm attaching the asm.ovlStore.err and the pacBioToCA log files for
complete descriptions of the error and the executed commands.

Thank you very much in advance.

Regards,
Santiago