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[wgs-assembler-users] correct-olaps error
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From: Zhou Qi <zh...@be...> - 2013-10-26 05:14:10
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Hi,
I’m using MaSuRCA assembler which takes CA6.0 as core and I got the some error message. Any input would be very much appreciated. My command is:
runCA gkpFixInsertSizes=0 jellyfishHashSize=10000000000 ovlRefBlockSize=1225516 ovlHashBlockSize=122551 ovlCorrBatchSize=40000000 utgErrorRate=0.03 merylMemory=8192 ovlMemory=8GB stopAfter=unitigger ovlMerThreshold=75 bogBreakAtIntersections=0 unitigger=bog bogBadMateDepth=1000000 -p genome -d CA merylThreads=32 frgCorrThreads=1 frgCorrConcurrency=48 cnsConcurrency=48 ovlCorrConcurrency=8 ovlConcurrency=48 ovlThreads=1 doFragmentCorrection=1 doOverlapBasedTrimming=1 doExtendClearRanges=2 ovlMerSize=22 superReadSequences_shr.frg /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/Genomic_reads/Dmir.female.454.frg f5.cor.clean.frg m5.cor.clean.frg f1.cor.clean.frg f2.cor.clean.frg m2.cor.clean.frg 1> runCA0.out 2>&1
and the error message is:
----------------------------------------END CONCURRENT Fri Oct 25 21:36:34 2013 (64 seconds)
Overlap correction job 1 (/jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/MaSuRCA-2.1.0/CA/3-overlapcorrection/0001) failed.
================================================================================
runCA failed.
----------------------------------------
Stack trace:
at /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/runCA line 1121
main::caFailure('1 overlap correction jobs failed; remove /jbods/data01/DATA/d...', undef) called at /jbods/data01/DATA/dmiran
da/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/runCA line 3019
main::overlapCorrection() called at /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/
bin/runCA line 5343
----------------------------------------
Failure message:
1 overlap correction jobs failed; remove /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/MaSuRCA-2.1.0/CA/3-overlapcorrection
/ovlcorr.sh (or run by hand) to try again
*** buffer overflow detected ***: /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps terminated
======= Backtrace: =========
/lib/libc.so.6(__fortify_fail+0x37)[0x7f474f7fcb47]
/lib/libc.so.6(+0xfea00)[0x7f474f7fba00]
/jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps[0x4030ee]
/jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps[0x40520c]
/lib/libc.so.6(__libc_start_main+0xfe)[0x7f474f71bd8e]
/jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps[0x402279]
======= Memory map: ========
00400000-00427000 r-xp 00000000 08:21 40083 /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps
00626000-00627000 r--p 00026000 08:21 40083 /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps
00627000-00628000 rw-p 00027000 08:21 40083 /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps
00628000-00636000 rw-p 00000000 00:00 0
01234000-68f4b000 rw-p 00000000 00:00 0 [heap]
7f46690d9000-7f46690da000 ---p 00000000 00:00 0
7f46690da000-7f4669ada000 rw-p 00000000 00:00 0
7f4669ada000-7f4669adb000 ---p 00000000 00:00 0
7f4669adb000-7f466a4db000 rw-p 00000000 00:00 0
7f466a4db000-7f466a4dc000 ---p 00000000 00:00 0
7f466a4dc000-7f466aedc000 rw-p 00000000 00:00 0
7f466b8dd000-7f474f6fd000 rw-p 00000000 00:00 0
7f474f6fd000-7f474f877000 r-xp 00000000 08:31 918102 /lib/libc-2.12.1.so
7f474f877000-7f474fa77000 ---p 0017a000 08:31 918102 /lib/libc-2.12.1.so
7f474fa77000-7f474fa7b000 r--p 0017a000 08:31 918102 /lib/libc-2.12.1.so
7f474fa7b000-7f474fa7c000 rw-p 0017e000 08:31 918102 /lib/libc-2.12.1.so
7f474fa7c000-7f474fa81000 rw-p 00000000 00:00 0
7f474fa81000-7f474fa96000 r-xp 00000000 08:31 917564 /lib/libgcc_s.so.1
7f474fa96000-7f474fc95000 ---p 00015000 08:31 917564 /lib/libgcc_s.so.1
7f474fc95000-7f474fc96000 r--p 00014000 08:31 917564 /lib/libgcc_s.so.1
7f474fc96000-7f474fc97000 rw-p 00015000 08:31 917564 /lib/libgcc_s.so.1
7f474fc97000-7f474fd19000 r-xp 00000000 08:31 918106 /lib/libm-2.12.1.so
7f474fd19000-7f474ff18000 ---p 00082000 08:31 918106 /lib/libm-2.12.1.so
7f474ff18000-7f474ff19000 r--p 00081000 08:31 918106 /lib/libm-2.12.1.so
7f474ff19000-7f474ff1a000 rw-p 00082000 08:31 918106 /lib/libm-2.12.1.so
7f474ff1a000-7f4750002000 r-xp 00000000 08:31 14684593 /usr/lib/libstdc++.so.6.0.14
7f4750002000-7f4750201000 ---p 000e8000 08:31 14684593 /usr/lib/libstdc++.so.6.0.14
7f4750201000-7f4750209000 r--p 000e7000 08:31 14684593 /usr/lib/libstdc++.so.6.0.14
7f4750209000-7f475020b000 rw-p 000ef000 08:31 14684593 /usr/lib/libstdc++.so.6.0.14
7f475020b000-7f4750220000 rw-p 00000000 00:00 0
7f4750220000-7f4750248000 r-xp 00000000 08:21 34381 /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/MaSuRCA-2.1.0/lib/libjellyfish-2.0.so.2.0.0
7f4750248000-7f4750448000 ---p 00028000 08:21 34381 /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/MaSuRCA-2.1.0/lib/libjellyfish-2.0.so.2.0.0
7f4750448000-7f4750449000 r--p 00028000 08:21 34381 /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/MaSuRCA-2.1.0/lib/libjellyfish-2.0.so.2.0.0
7f4750449000-7f475044a000 rw-p 00029000 08:21 34381 /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/MaSuRCA-2.1.0/lib/libjellyfish-2.0.so.2.0.0
7f475044a000-7f4750462000 r-xp 00000000 08:31 918123 /lib/libpthread-2.12.1.so
7f4750462000-7f4750661000 ---p 00018000 08:31 918123 /lib/libpthread-2.12.1.so
7f4750661000-7f4750662000 r--p 00017000 08:31 918123 /lib/libpthread-2.12.1.so
7f4750662000-7f4750663000 rw-p 00018000 08:31 918123 /lib/libpthread-2.12.1.so
7f4750663000-7f4750667000 rw-p 00000000 00:00 0
7f4750667000-7f4750687000 r-xp 00000000 08:31 918051 /lib/ld-2.12.1.so
7f475085b000-7f4750861000 rw-p 00000000 00:00 0
7f4750878000-7f4750887000 rw-p 00000000 00:00 0
7f4750887000-7f4750888000 r--p 00020000 08:31 918051 /lib/ld-2.12.1.so
7f4750888000-7f4750889000 rw-p 00021000 08:31 918051 /lib/ld-2.12.1.so
7f4750889000-7f475088a000 rw-p 00000000 00:00 0
7fff824ab000-7fff824cd000 rw-p 00000000 00:00 0 [stack]
7fff82583000-7fff82584000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] |
