Menu ▾ ▴

#342 overlapStoreBuild failed

overlapper
open
nobody
None
5
2021-12-07
2021-12-07
Ling Jin
No

Dear all,
I run CeleraAssembler using 60 G bp next-sequencing data, and I come into and error when building overlap store after 1-overlapper. I am wondering if I have run out of memory. Are there any recommendations for changing the parameters? I have also attach my spec_file below. This is part of my log file:

----------------------------------------START Mon Dec  6 20:30:41 2021
/public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/gatekeeper  -o /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.gkpStore.BUILDING  /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/Tbrevi-01F_notCombined.frg /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/Tbrevi-01F_extendedFrags.frg > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.gkpStore.err 2>&1
----------------------------------------END Mon Dec  6 20:57:44 2021 (1623 seconds)
numFrags = 341784124
No need to run meryl for OBT (OBT is disabled).
----------------------------------------START Mon Dec  6 20:57:44 2021
/public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/meryl  -B -C -v -m 22 -memory 320000 -threads 60 -c 0  -L 2  -s /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.gkpStore:chain  -o /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./0-mercounts/Tbrevi-01F-C-ms22-cm0 > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./0-mercounts/meryl.err 2>&1
----------------------------------------END Mon Dec  6 22:44:57 2021 (6433 seconds)
----------------------------------------START Mon Dec  6 22:44:57 2021
/public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/estimate-mer-threshold  -m /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./0-mercounts/Tbrevi-01F-C-ms22-cm0  > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./0-mercounts/Tbrevi-01F-C-ms22-cm0.estMerThresh.out 2> /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./0-mercounts/Tbrevi-01F-C-ms22-cm0.estMerThresh.err
----------------------------------------END Mon Dec  6 22:44:57 2021 (0 seconds)
----------------------------------------START Mon Dec  6 22:44:57 2021
/public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/meryl -Dt -n 5134 -s /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./0-mercounts/Tbrevi-01F-C-ms22-cm0 > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./0-mercounts/Tbrevi-01F.nmers.ovl.fasta 2> /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./0-mercounts/Tbrevi-01F.nmers.ovl.fasta.err 
----------------------------------------END Mon Dec  6 22:45:28 2021 (31 seconds)
Reset OVL mer threshold from  to 5134.
----------------------------------------START Mon Dec  6 22:45:29 2021
/public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/overlap_partition \
 -g  /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.gkpStore \
 -bl 1000000000 \
 -bs 0 \
 -rs 24000000 \
 -rl 0 \
 -o  /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper \
> /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/overlap_partition.err 2>&1
----------------------------------------END Mon Dec  6 22:45:46 2021 (17 seconds)
Created 462 overlap jobs.  Last batch '001', last job '000462'.
----------------------------------------START CONCURRENT Mon Dec  6 22:45:46 2021
/public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/overlap.sh 1 > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/000001.out 2>&1
/public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/overlap.sh 2 > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/000002.out 2>&1
...omitting about 400 lines here
/public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/overlap.sh 461 > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/000461.out 2>&1
/public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/overlap.sh 462 > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/000462.out 2>&1
----------------------------------------END CONCURRENT Tue Dec  7 09:04:31 2021 (37125 seconds)
----------------------------------------START Tue Dec  7 09:04:36 2021
find -L /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper \( -name \*ovb.gz -or -name \*ovb \) -print > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.ovlStore.list
----------------------------------------END Tue Dec  7 09:04:41 2021 (5 seconds)
----------------------------------------START Tue Dec  7 09:04:41 2021
/public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild  -o /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.ovlStore.BUILDING  -g /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.gkpStore  -M 500000 -L /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.ovlStore.list  > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.ovlStore.err 2>&1
sh: line 1: 77876 Aborted                 /public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild -o /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.ovlStore.BUILDING -g /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.gkpStore -M 500000 -L /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.ovlStore.list > /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.ovlStore.err 2>&1
----------------------------------------END Tue Dec  7 16:05:22 2021 (25241 seconds)
ERROR: Failed with signal ABRT (6)
================================================================================

runCA failed.

----------------------------------------
Stack trace:

 at /public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/runCA line 1628, <J> line 462.
    main::caFailure("failed to create the overlap store", "/public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-"...) called at /public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/runCA line 3696
    main::createOverlapStore() called at /public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/runCA line 6255

----------------------------------------
Last few lines of the relevant log file (/public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./Tbrevi-01F.ovlStore.err):

bucketizing /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/001/000349.ovb.gz
bucketizing /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/001/000127.ovb.gz
bucketizing /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/001/000099.ovb.gz
bucketizing /public1/home/sc61333/project/gaoyuanqiu/Tbrevi-01F/./1-overlapper/001/000347.ovb.gz
bucketizing DONE!
overlaps skipped:
               0 OBT - low quality
               0 DUP - non-duplicate overlap
               0 DUP - different library
               0 DUP - dedup not requested
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc

Failed with 'Aborted'

Backtrace (mangled):

/public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild(_Z17AS_UTL_catchCrashiP9siginfo_tPv+0x2a)[0x40945a]
/lib64/libpthread.so.0(+0xf630)[0x2b71ec0ec630]
/lib64/libc.so.6(gsignal+0x37)[0x2b71ec32f387]
/lib64/libc.so.6(abort+0x148)[0x2b71ec330a78]
/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x165)[0x2b71eb6f7a95]
/lib64/libstdc++.so.6(+0x5ea06)[0x2b71eb6f5a06]
/lib64/libstdc++.so.6(+0x5ea33)[0x2b71eb6f5a33]
/lib64/libstdc++.so.6(+0x5ec53)[0x2b71eb6f5c53]
/lib64/libstdc++.so.6(_Znwm+0x7d)[0x2b71eb6f61ed]
/lib64/libstdc++.so.6(_Znam+0x9)[0x2b71eb6f6289]
/public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild(main+0x1450)[0x4067a0]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b71ec31b555]
/public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild[0x406a8d]

Backtrace (demangled):

[0] /public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild::AS_UTL_catchCrash(int, siginfo_t*, void*) + 0x2a  [0x40945a]
[1] /lib64/libpthread.so.0::(null) + 0xf630  [0x2b71ec0ec630]
[2] /lib64/libc.so.6::(null) + 0x37  [0x2b71ec32f387]
[3] /lib64/libc.so.6::(null) + 0x148  [0x2b71ec330a78]
[4] /lib64/libstdc++.so.6::__gnu_cxx::__verbose_terminate_handler() + 0x165  [0x2b71eb6f7a95]
[5] /lib64/libstdc++.so.6::(null) + 0x5ea06  [0x2b71eb6f5a06]
[6] /lib64/libstdc++.so.6::(null) + 0x5ea33  [0x2b71eb6f5a33]
[7] /lib64/libstdc++.so.6::(null) + 0x5ec53  [0x2b71eb6f5c53]
[8] /lib64/libstdc++.so.6::operator new(unsigned long) + 0x7d  [0x2b71eb6f61ed]
[9] /lib64/libstdc++.so.6::operator new[](unsigned long) + 0x9  [0x2b71eb6f6289]
[10] /public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild::(null) + 0x1450  [0x4067a0]
[11] /lib64/libc.so.6::(null) + 0xf5  [0x2b71ec31b555]
[12] /public1/home/sc61333/software/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild() [0x406a8d]

GDB:



----------------------------------------
Failure message:

failed to create the overlap store

This is my spec_file for running runAC:

ovlConcurrency=7
ovlThreads=12
cnsConcurrency =60
merSize=22
merylMemory=320000
merylThreads=60
# merThreshold=5000
doOBT=0
overlapper=ovl
ovlStoreMemory = 500000
ovlRefBlockSize = 24000000
ovlHashBits = 26
ovlHashBlockLength = 1000000000
doFragmentCorrection=0
unitigger=bogart
batMemory=320
batThreads = 60
doExtendClearRanges=0
doToggle = 0
gkpFixInsertSizes=0
Tbrevi-01F_notCombined.frg
Tbrevi-01F_extendedFrags.frg

Discussion

Log in to post a comment.

MongoDB Logo MongoDB