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#342 overlapStoreBuild failed
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