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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...> - 2013-08-29 06:54:09
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Hi Brian,
thanks again.
Somehow the output begins to make less sense now.
I've recompiled the assembler with the debug option (don't see any line numbers mentioned anywhere though), and suddenly I get
- an assembly without problems with the PacBio data
- a failure in gatekeeper (while using runCA...???) if I try to run the matepair data
- a failure at read deduplication if I run it with PacBio and matepair data
I use the .frg files, which I've produced with the stable version, in case that makes a difference.
For the gatekeeper error:
bastian@SSB13002:~/Tools/wgs-svn/Linux-amd64/bin$ ./runCA -d test_dir -p test_prefix /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/mate_pair.frg
----------------------------------------START Thu Aug 29 08:32:23 2013
/home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper -o /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test_dir/test_prefix.gkpStore.BUILDING -T -F /home/bastian/Tools/wgs-7.0/Linux-amd64/bin/mate_pair.frg > /home/bastian/Tools/wgs-svn/Linux-amd64/bin/test_dir/test_prefix.gkpStore.err 2>&1
----------------------------------------END Thu Aug 29 08:32:55 2013 (32 seconds)
ERROR: Failed with signal ABRT (6)
================================================================================
runCA failed.
----------------------------------------
Stack trace:
at ./runCA line 1418
main::caFailure('gatekeeper failed', '/home/bastian/Tools/wgs-svn/Linux-amd64/bin/test_dir/test_pre...') called at ./runCA line 1741
main::preoverlap('/home/bastian/Tools/wgs-7.0/Linux-amd64/bin/mate_pair.frg') called at ./runCA line 6116
----------------------------------------
Last few lines of the relevant log file (/home/bastian/Tools/wgs-svn/Linux-amd64/bin/test_dir/test_prefix.gkpStore.err):
[0] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper::AS_UTL_catchCrash(int, siginfo*, void*) + 0x34 [0x435c9e]
[1] /lib/x86_64-linux-gnu/libpthread.so.0::(null) + 0xfcb0 [0x7fc5763c2cb0]
[2] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x35 [0x7fc57602a425]
[3] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x17b [0x7fc57602db8b]
[4] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2f0ee [0x7fc5760230ee]
[5] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2f192 [0x7fc576023192]
[6] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper::gkStore::gkStore_computeRanges(unsigned int, unsigned int, long&, long&, long&, long&, long&, long&, long&, long&, long&) + 0x101 [0x4649dd]
[7] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper::gkStream::reset(unsigned int, unsigned int) + 0x244 [0x45fb24]
[8] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper::gkStream::gkStream(gkStore*, unsigned int, unsigned int, unsigned int) + 0xc4 [0x45f850]
[9] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper::gkStoreStats::init(gkStore*) + 0x5a [0x45d844]
[10] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper::gkStoreStats::gkStoreStats(gkStore*) + 0x23 [0x45d7e7]
[11] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper::AS_GKP_summarizeErrors(char*) + 0x79 [0x42aaa2]
[12] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper::(null) + 0x1bd3 [0x40fed4]
[13] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0xed [0x7fc57601576d]
[14] /home/bastian/Tools/wgs-svn/Linux-amd64/bin/gatekeeper() [0x40a9b9]
GDB:
Aborted (core dumped)
----------------------------------------
Failure message:
gatekeeper failed
Related gkpStore.err attached, related errorLog is empty, related gatekeeper log attached.
Permissions (no .gpkStore folder created):
bastian@SSB13002:~/Tools/wgs-svn/Linux-amd64/bin$ ls -l test_dir/
total 16
-rw-rw-r-- 1 bastian bastian 3391 Aug 29 08:40 gatekeeper_failure_test_prefix.gkpStore.err
drwxr-xr-x 2 bastian bastian 4096 Aug 29 08:32 runCA-logs
drwxrwxr-x 2 bastian bastian 4096 Aug 29 08:32 test_prefix.gkpStore.BUILDING
-rw-rw-r-- 1 bastian bastian 0 Aug 29 08:32 test_prefix.gkpStore.BUILDING.errorLog
-rw-rw-r-- 1 bastian bastian 0 Aug 29 08:32 test_prefix.gkpStore.BUILDING.fastqUIDmap
-rw-rw-r-- 1 bastian bastian 3416 Aug 29 08:40 test_prefix.gkpStore.err~
The related data for the error when I run both datasets combined:
The command line output is attached.
Related gkpStore.err attached, related errorLog is empty, related deduplicate.err attached.
Permissions:
bastian@SSB13002:~/Tools/wgs-svn/Linux-amd64/bin/test_dir_combined$ ls -l *gkpStore
total 9800
-rw-rw-r-- 1 bastian bastian 14800 Aug 29 08:44 clr-NORMAL-01-CLR
-rw-rw-r-- 1 bastian bastian 20 Aug 29 08:44 f2p
-rw-rw-r-- 1 bastian bastian 177632 Aug 29 08:44 fnm
-rw-rw-r-- 1 bastian bastian 80 Aug 29 08:44 fpk
-rw-rw-r-- 1 bastian bastian 80 Aug 29 08:44 fsb
-rw-rw-r-- 1 bastian bastian 144 Aug 29 08:44 inf
-rw-rw-r-- 1 bastian bastian 512 Aug 29 08:44 lib
-rw-rw-r-- 1 bastian bastian 80 Aug 29 08:44 plc
-rw-rw-r-- 1 bastian bastian 7723868 Aug 29 08:44 qnm
-rw-rw-r-- 1 bastian bastian 80 Aug 29 08:44 qpk
-rw-rw-r-- 1 bastian bastian 80 Aug 29 08:44 qsb
-rw-rw-r-- 1 bastian bastian 1949980 Aug 29 08:44 snm
-rw-rw-r-- 1 bastian bastian 80 Aug 29 08:44 ssb
-rw-rw-r-- 1 bastian bastian 118452 Aug 29 08:44 u2i
-rw-rw-r-- 1 bastian bastian 115 Aug 29 08:44 uid
This is somehow getting a bit strange now.
And not sure if I'm really helpful at the moment.
Still hope to get some more ideas.
Thanks already.
Bastian
________________________________________
From: Walenz, Brian [bw...@jc...]
Sent: Wednesday, August 28, 2013 4:44 PM
To: Hornung, Bastian; wgs...@li...
Subject: Re: [wgs-assembler-users] Problem with the overlapper, "AS_OVS_openBinaryOverlapFile()-- Failed to open..."
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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