Re: [wgs-assembler-users] Problem with the overlapper, "AS_OVS_openBinaryOverlapFile()-- Failed to

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It seems to have made it further.  It no longer complains about no overlaps,
but seems to be failing an assert trying to delete a read.  I've never seen
that before.

Was this a full restart with the new code?

Can you post a bit more of the err log, and 'ls -l *gkpStore' (to check for
permissions and extraneous files).

The most information will be to recompile with debug (cd wgs-svn/src ; rm
-rf ../Linux-amd64 ; gmake BUILDDEBUG=1) and rerun.  This will populate the
crash report with line numbers.

b

On 8/28/13 7:50 AM, "Hornung, Bastian" <bas...@wu...> wrote:

> 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.deduplicat
> e.log \
> -summary 
> /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/0-overlaptrim/test.deduplicat
> e.summary \
>> /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test/0-overlaptrim/test.deduplica
>> te.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.deduplica
> te.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_delF
> ragment(unsigned int, bool) + 0xd8  [0x40f678]
> [8] 
> /home/bastian/Tools/wgs-svn/Linux-amd64/bin/deduplicate::deleteFragments(gkSto
> re*, 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_an>>
d
>> _mate_pair.gkpStore \
>> -ovs
>> 
/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlap>>
t
>> rim/PacBio_and_mate_pair.obtStore \
>> -ovs
>> 
/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlap>>
t
>> rim/PacBio_and_mate_pair.dupStore \
>> -report
>> 
/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlap>>
t
>> rim/PacBio_and_mate_pair.deduplicate.log \
>> -summary
>> 
/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overlap>>
t
>> rim/PacBio_and_mate_pair.deduplicate.summary \
>>> 
/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/test2.gpkStore/assembly/0-overla>>>
p
>>> 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-overla>>
p
>> 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-overla>>
p
>> 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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> 
> 
> 
> 
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Re: [wgs-assembler-users] Problem with the overlapper, "AS_OVS_openBinaryOverlapFile()-- Failed to

Re: [wgs-assembler-users] Problem with the overlapper, "AS_OVS_openBinaryOverlapFile()-- Failed to open..."