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

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

Thank you very much for your reply. Actually you are right, I had run out
of disk space so the file was incomplete. I ran that step again after I had
released some more space and the program finished successfully.
Thanks!

On Fri, Dec 12, 2014 at 2:38 AM, Brian Walenz <th...@gm...> wrote:

> That's a new one!  I'm guessing that the file (of overlaps, ".ovb.gz"
> probably) it is reading was truncated.  Delete either the overlap files in
> 1-overlapper or just the whole 1-overlapper directory and restart.
>
> Better yet, save the existing ovb's in a subdirectory, restart, and
> compare.  Hopefully one of the older ones will be smaller.  You might need
> to ungzip them first.  If it still fails, and the files are the same, then
> we know there's an actual problem somewhere.
>
> b
>
>
>
> On Thu, Dec 11, 2014 at 1:37 PM, carlos vargas <cha...@gm...> wrote:
>
>> 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)
>>
>>