Re: [wgs-assembler-users] Problem with PBcR when cleaning PacBio reads

[carlos v. <cha...@gm...>]

Thanks a lot! I installed blasr as you suggested and the mapping was
performed and the .ovb files were obtained, however now I have a new
problem, is it a problem of memory? The error message is the following:


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

Failed with 'Aborted'

Backtrace (mangled):

/home/cvargas/wgs-8.2/Linux-amd64/bin/overlapStoreBuild(_Z17AS_UTL_catchCrashiP7siginfoPv+0x27)[0x40a697]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)[0x7f7860d6fcb0]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35)[0x7f78609d70d5]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x17b)[0x7f78609da83b]
/lib/x86_64-linux-gnu/libc.so.6(+0x2ed9e)[0x7f78609cfd9e]
/lib/x86_64-linux-gnu/libc.so.6(+0x2ee42)[0x7f78609cfe42]
/home/cvargas/wgs-8.2/Linux-amd64/bin/overlapStoreBuild[0x411dbd]
/home/cvargas/wgs-8.2/Linux-amd64/bin/overlapStoreBuild(main+0x7e6)[0x405b56]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f78609c276d]
/home/cvargas/wgs-8.2/Linux-amd64/bin/overlapStoreBuild[0x405059]

Backtrace (demangled):

[0]
/home/cvargas/wgs-8.2/Linux-amd64/bin/overlapStoreBuild::AS_UTL_catchCrash(int,
siginfo*, void*) + 0x27  [0x40a697]
[1] /lib/x86_64-linux-gnu/libpthread.so.0::(null) + 0xfcb0  [0x7f7860d6fcb0]
[2] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x35  [0x7f78609d70d5]
[3] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x17b  [0x7f78609da83b]
[4] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2ed9e  [0x7f78609cfd9e]
[5] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2ee42  [0x7f78609cfe42]
[6] /home/cvargas/wgs-8.2/Linux-amd64/bin/overlapStoreBuild() [0x411dbd]
[7] /home/cvargas/wgs-8.2/Linux-amd64/bin/overlapStoreBuild::(null) + 0x7e6
 [0x405b56]
[8] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0xed  [0x7f78609c276d]
[9] /home/cvargas/wgs-8.2/Linux-amd64/bin/overlapStoreBuild() [0x405059]

GDB:


Aborted (core dumped)

On Mon, Dec 8, 2014 at 9:36 PM, Serge Koren <ser...@gm...> wrote:

> Hi,
>
> This error is caused by a missing component of BLASR (sawriter) not being
> available in your path. It looks like you’re using BLASR which is packaged
> with the SSPACE scaffolder so I’m not sure if they include the full BLASR
> package. I would suggest downloading/compiling BLASR directly from GitHub
> and adding it to your path to ensure the full package is available.
>
> Sergey
>
> > On Dec 8, 2014, at 3:22 PM, carlos vargas <cha...@gm...> wrote:
> >
> > Hello,
> >
> > I have been trying to clean some PacBio reads using Illumina reads with
> PBcR. However it has been failing during the overlapper. It builds several
> files using the Illumina reads, however when it fails it gives the
> following message:
> >
> > ----------------------------------------END CONCURRENT Mon Dec  8
> 20:52:43 2014 (3695 seconds)
> > ERROR:  Overlap prep job
> Illumina/PE/CA//temppacbio/1-overlapper/long_reads_part    1 FAILED.
> > ERROR:  Overlap prep job
> Illumina/PE/CA//temppacbio/1-overlapper/long_reads_part    2 FAILED.
> >
> > 2 overlap partitioning jobs failed.
> >
> > In 1-overlapper there is the following message in the 24.hash.err:
> >
> > /usr/bin/time: cannot run
> /home/local_installs/software/SSPACE-LongRead/sawriter: No such file or
> directory
> > Command exited with non-zero status 127
> > 0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata
> 2112maxresident)k
> > 0inputs+8outputs (0major+83minor)pagefaults 0swaps
> >
> > However it seems it is not a problem as it has it performs every step
> until reaching that step. Any idea as to what might be the problem?
> >
> > Thanks in advance,
> > Carlos
> >
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