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Re: [wgs-assembler-users] Problem with the overlapper, "AS_OVS_openBinaryOverlapFile()-- Failed to open..."
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From: Hornung, B. <bas...@wu...> - 2013-08-28 11:51:07
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Sorry, should probably go over the mailing list.
Thanks for the further help Brian.
Forgot to "make install" (should've read the readme).
It doesn't go further though, just more details in the command line:
----------------------------------------START Wed Aug 28 13:43:07 2013
/home/bastian/Tools/wgs-svn/Linux-amd64/bin/deduplicate \
-gkp /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/test.gkpStore \
-ovs /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/0-overlaptrim/test.obtStore \
-ovs /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/0-overlaptrim/test.dupStore \
-report /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/0-overlaptrim/test.deduplicate.log \
-summary /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/0-overlaptrim/test.deduplicate.summary \
> /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/0-overlaptrim/test.deduplicate.err 2>&1
----------------------------------------END Wed Aug 28 13:43:09 2013 (2 seconds)
ERROR: Failed with signal ABRT (6)
================================================================================
runCA failed.
----------------------------------------
Stack trace:
at ./runCA line 1418
main::caFailure('failed to deduplicate the reads', '/home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/0-overlaptri...') called at ./runCA line 3911
main::overlapTrim() called at ./runCA line 6118
----------------------------------------
Last few lines of the relevant log file (/home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/0-overlaptrim/test.deduplicate.err):
Backtrace (demangled):
[0] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/deduplicate::AS_UTL_catchCrash(int, siginfo*, void*) + 0x24 [0x408824]
[1] /lib/x86_64-linux-gnu/libpthread.so.0::(null) + 0xfcb0 [0x7fe93d576cb0]
[2] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x35 [0x7fe93d1de425]
[3] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x17b [0x7fe93d1e1b8b]
[4] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2f0ee [0x7fe93d1d70ee]
[5] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2f192 [0x7fe93d1d7192]
[6] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/deduplicate() [0x40ea54]
[7] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/deduplicate::gkStore::gkStore_delFragment(unsigned int, bool) + 0xd8 [0x40f678]
[8] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/deduplicate::deleteFragments(gkStore*, fragT*) + 0x49 [0x406de9]
[9] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/deduplicate::(null) + 0xa1c [0x40553c]
[10] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0xed [0x7fe93d1c976d]
[11] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/deduplicate() [0x4055a9]
GDB:
Aborted (core dumped)
----------------------------------------
Failure message:
failed to deduplicate the reads
Seems that it has nothing to do with the PacBio data, but the mate pair data causes the crash.
You mentioned that this could mean that there could just not be any duplicated reads...er...that's good for the library, isn't it?
Thanks for any further thoughts,
Bastian
________________________________________
From: Walenz, Brian [bw...@jc...]
Sent: Wednesday, August 28, 2013 12:22 PM
To: Hornung, Bastian
Subject: Re: [wgs-assembler-users] Problem with the overlapper, "AS_OVS_openBinaryOverlapFile()-- Failed to open..."
I'm guessing this indicates two problems:
1) you don't have kmer installed.
2) AS_MER_meryl.cc (an obsolete version that compiles if kmer isn't
installed) is broken.
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Check_ou
t_and_Compile
On 8/28/13 3:25 AM, "Hornung, Bastian" <bas...@wu...> wrote:
> Hi Brian,
>
> t runs with both the suggested options, thanks.
>
> I've also tried the latest unstable version, and it doesn't compile (...and my
> C++ skills are underwhelming, can't fix it myself...).
> ############################## AS_MER ##############################
> make[1]: *** No rule to make target `AS_global.h', needed by `AS_MER_meryl.o'.
> Stop.
> make: *** [objs] Error 1
>
> I guess I'll now have to do some quality checking...
>
> thanks for the help,
>
> Bastian
>
> ________________________________________
> From: Walenz, Brian [bw...@jc...]
> Sent: Tuesday, August 27, 2013 5:57 PM
> To: Hornung, Bastian; wgs...@li...
> Subject: RE: [wgs-assembler-users] Problem with the overlapper,
> "AS_OVS_openBinaryOverlapFile()-- Failed to open..."
>
> Hi-
>
> It is complaining that there are no overlaps in the 'dupStore'. This could
> mean store creation failed, but it probably just means there are no duplicate
> reads.
>
> Can you upgrade to the latest 'unstable' version in subversion and rerun? If
> it still fails, I should be able to fix easily. I think it might be fixed
> already.
>
> Alternatively, you can disable all trimming (doOBT=0) or just dedupe
> (doDeDuplication=0). Odd that it worked with just the pacbio!
>
> b
>
>
> ________________________________________
> From: Hornung, Bastian [bas...@wu...]
> Sent: Tuesday, August 27, 2013 7:16 AM
> To: wgs...@li...
> Subject: [wgs-assembler-users] Problem with the overlapper,
> "AS_OVS_openBinaryOverlapFile()-- Failed to open..."
>
> Hi @all,
>
> sorry if that's the wrong way, but I have a problem with the wgs assembler,
> and not really an idea if there's a bug or if I'm just dumb and doing
> something wrong (first time I use it).
>
> I'm trying to run an assembly with PacBio short reads and illumina mate pair
> reads, and during the assembly runCA aborts, due to a failure in the
> overlapper.
> I've converted my data to 2 .frg files, then I've run gatekeeper with both,
> which worked without errors (well...sort of, had to compile it myself, due to
> https://sourceforge.net/p/wgs-assembler/bugs/253/ ).
> Then I run runCA, which then crashes because it can't deduplicate the reads.
>
> Parts of the command line output:
>
> ----------------------------------------START Tue Aug 27 12:58:34 2013
> /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/deduplicate \
> -gkp
> /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/PacBio_and
> _mate_pair.gkpStore \
> -ovs
> /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlapt
> rim/PacBio_and_mate_pair.obtStore \
> -ovs
> /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlapt
> rim/PacBio_and_mate_pair.dupStore \
> -report
> /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlapt
> rim/PacBio_and_mate_pair.deduplicate.log \
> -summary
> /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlapt
> rim/PacBio_and_mate_pair.deduplicate.summary \
>> /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlap
>> trim/PacBio_and_mate_pair.deduplicate.err 2>&1
> ----------------------------------------END Tue Aug 27 12:58:34 2013 (0
> seconds)
> ERROR: Failed with signal HUP (1)
> ==============================================================================
> ==
>
> runCA failed.
>
> ----------------------------------------
> Stack trace:
>
> at ./runCA line 1237
> main::caFailure('failed to deduplicate the reads',
> '/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkSto...') called at
> ./runCA line 3739
> main::overlapTrim() called at ./runCA line 5876
>
> ----------------------------------------
> Last few lines of the relevant log file
> (/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlap
> trim/PacBio_and_mate_pair.deduplicate.err):
>
> AS_OVS_openBinaryOverlapFile()-- Failed to open
> '/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlap
> trim/PacBio_and_mate_pair.dupStore/0001' for reading: No such file or
> directory
>
> ----------------------------------------
> Failure message:
>
> failed to deduplicate the reads
>
>
> I have absolutely no clue what could be happening here.
> If I run it with only the PacBio data, then it works, so the installation
> itself is okay.
>
> Any advice?
>
> Best regards,
>
> Bastian
>
>
>
>
>
>
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