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

[Brian W. <th...@gm...>]

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)
>
>