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[wgs-assembler-users] pacBioToCA: caFailure('can\'t set both ovlRefBlockSize and ovlRefBlockLength'
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From: Adrian P. <ape...@gm...> - 2015-03-26 00:55:14
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Hello,
My run ends with this bizarre error (see below). I ran:
~/programs/wgs-8.3rc1/Linux-amd64/bin/pacBioToCA -length 500 -partitions
200 -l ec_pacbio -t 16 -s pacbio.spec -fastq PacBio.fastq Lib3_PE.frg >
run.out 2>&1
and my pacbio.spec is:
stopAfter=overlapper
# original asm settings
utgErrorRate = 0.25
utgErrorLimit = 4.5
cnsErrorRate = 0.25
cgwErrorRate = 0.25
ovlErrorRate = 0.25
merSize=14
merylMemory = 128000
merylThreads = 16
ovlStoreMemory = 8192
# grid info
useGrid = 0
scriptOnGrid = 0
frgCorrOnGrid = 0
ovlCorrOnGrid = 0
sge = -A assembly
sgeScript = -pe threads 16
sgeConsensus = -pe threads 1
sgeOverlap = -pe threads 2
sgeFragmentCorrection = -pe threads 2
sgeOverlapCorrection = -pe threads 1
#ovlMemory=8GB --hashload 0.7
ovlHashBits = 25
ovlThreads = 2
ovlHashBlockLength = 20000000
ovlRefBlockSize = 50000000
# for mer overlapper
merCompression = 1
merOverlapperSeedBatchSize = 500000
merOverlapperExtendBatchSize = 250000
frgCorrThreads = 2
frgCorrBatchSize = 100000
ovlCorrBatchSize = 100000
# non-Grid settings, if you set useGrid to 0 above these will be used
merylMemory = 128000
merylThreads = 4
ovlStoreMemory = 8192
ovlConcurrency = 8
cnsConcurrency = 8
merOverlapperThreads = 3
merOverlapperSeedConcurrency = 3
merOverlapperExtendConcurrency = 3
frgCorrConcurrency = 2
ovlCorrConcurrency = 4
cnsConcurrency = 4
LOG:
tail run.out -f
----------------------------------------START Wed Mar 25 18:47:55 2015
mkdir tempec_pacbio
----------------------------------------END Wed Mar 25 18:47:55 2015 (0
seconds)
----------------------------------------START Wed Mar 25 18:47:55 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/fastqToCA -libraryname
ec_pacbio -type sanger -technology none -feature doConsensusCorrection 1
-reads /home/adrian/Rozella/reads/PacBio.fastq >
/home/adrian/Rozella/reads//tempec_pacbio/ec_pacbio.frg
----------------------------------------END Wed Mar 25 18:47:55 2015 (0
seconds)
----------------------------------------START Wed Mar 25 18:47:55 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/runCA -s
/home/adrian/Rozella/reads//tempec_pacbio/ec_pacbio.spec -p asm -d
tempec_pacbio stopAfter=initialStoreBuilding
/home/adrian/Rozella/reads/Lib3_PE.frg
/home/adrian/Rozella/reads//tempec_pacbio/ec_pacbio.frg
----------------------------------------START Wed Mar 25 18:47:55 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/gatekeeper -o
/home/adrian/Rozella/reads/tempec_pacbio/asm.gkpStore.BUILDING -F
/home/adrian/Rozella/reads/Lib3_PE.frg
/home/adrian/Rozella/reads//tempec_pacbio/ec_pacbio.frg >
/home/adrian/Rozella/reads/tempec_pacbio/asm.gkpStore.err 2>&1
----------------------------------------END Wed Mar 25 18:53:44 2015
(349 seconds)
numFrags = 22786178
Stop requested after 'initialstorebuilding'.
----------------------------------------END Wed Mar 25 18:53:44 2015
(349 seconds)
Will be correcting PacBio library 2 with librarie[s] 1 - 1
----------------------------------------START Wed Mar 25 18:53:53 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/gatekeeper
-dumpfragments -invert -tabular -longestovermin 2 500 -longestlength 2
412825510 /home/adrian/Rozella/reads//tempec_pacbio/asm.gkpStore 2>
/home/adrian/Rozella/reads//tempec_pacbio/asm.seedlength |awk '{if
(!(match($1, "UID") != 0 && length($1) == 3)) { print "frg uid "$1"
isdeleted 1"; } }' >
/home/adrian/Rozella/reads//tempec_pacbio/asm.toerase.uid
----------------------------------------END Wed Mar 25 18:54:00 2015 (7
seconds)
----------------------------------------START Wed Mar 25 18:54:00 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/gatekeeper --edit
/home/adrian/Rozella/reads//tempec_pacbio/asm.toerase.uid
/home/adrian/Rozella/reads//tempec_pacbio/asm.gkpStore >
/home/adrian/Rozella/reads//tempec_pacbio/asm.toerase.out 2>
/home/adrian/Rozella/reads//tempec_pacbio/asm.toerase.err
----------------------------------------END Wed Mar 25 18:54:05 2015 (5
seconds)
Running with 370260486 bp for ec_pacbio.
Correcting with 3013291715 bp.
----------------------------------------START Wed Mar 25 18:54:08 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/runCA -s
/home/adrian/Rozella/reads//tempec_pacbio/ec_pacbio.spec -p asm -d
tempec_pacbio ovlHashLibrary=2 ovlRefLibrary=1-1 ovlCheckLibrary=1
obtHashLibrary=1-1 obtRefLibrary=1-1 obtCheckLibrary=0
doOverlapBasedTrimming=0 stopAfter=meryl
No need to run meryl for OBT (OBT is disabled).
----------------------------------------START Wed Mar 25 18:54:08 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/meryl -B -C -v -m 14
-memory 128000 -threads 16 -c 0 -L 2 -s
/home/adrian/Rozella/reads/tempec_pacbio/asm.gkpStore:chain -o
/home/adrian/Rozella/reads/tempec_pacbio/0-mercounts/asm-C-ms14-cm0 >
/home/adrian/Rozella/reads/tempec_pacbio/0-mercounts/meryl.err 2>&1
----------------------------------------END Wed Mar 25 19:17:17 2015
(1389 seconds)
----------------------------------------START Wed Mar 25 19:17:17 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/estimate-mer-threshold
-m /home/adrian/Rozella/reads/tempec_pacbio/0-mercounts/asm-C-ms14-cm0 >
/home/adrian/Rozella/reads/tempec_pacbio/0-mercounts/asm-C-ms14-cm0.estMerThresh.out
2>
/home/adrian/Rozella/reads/tempec_pacbio/0-mercounts/asm-C-ms14-cm0.estMerThresh.err
----------------------------------------END Wed Mar 25 19:17:17 2015 (0
seconds)
----------------------------------------START Wed Mar 25 19:17:17 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/meryl -Dt -n 503 -s
/home/adrian/Rozella/reads/tempec_pacbio/0-mercounts/asm-C-ms14-cm0 >
/home/adrian/Rozella/reads/tempec_pacbio/0-mercounts/asm.nmers.ovl.fasta
2>
/home/adrian/Rozella/reads/tempec_pacbio/0-mercounts/asm.nmers.ovl.fasta.err
----------------------------------------END Wed Mar 25 19:17:26 2015 (9
seconds)
Reset OVL mer threshold from to 503.
Stop requested after 'meryl'.
----------------------------------------END Wed Mar 25 19:17:26 2015
(1398 seconds)
----------------------------------------START Wed Mar 25 19:17:26 2015
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/runCA -s
/home/adrian/Rozella/reads//tempec_pacbio/ec_pacbio.spec -p asm -d .
ovlMerThreshold=503 ovlHashLibrary=2 ovlRefLibrary=1-1 ovlCheckLibrary=1
obtHashLibrary=1-1 obtRefLibrary=1-1 obtCheckLibrary=0
gridEnginePropagateHold="pBcR_asm" stopAfter=overlapper
No need to run meryl for OBT (OBT is disabled).
No need to run meryl for OVL (asm.nmers.ovl.fasta exists).
================================================================================
runCA failed.
----------------------------------------
Stack trace:
at /home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/runCA line 1649.
main::caFailure('can\'t set both ovlRefBlockSize and
ovlRefBlockLength', undef) called at
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/runCA line 3789
main::createOverlapJobs('normal') called at
/home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/runCA line 6554
----------------------------------------
Failure message:
can't set both ovlRefBlockSize and ovlRefBlockLength
----------------------------------------END Wed Mar 25 19:17:26 2015 (0
seconds)
Failed to execute /home/adrian/programs/wgs-8.3rc1/Linux-amd64/bin/runCA
-s /home/adrian/Rozella/reads//tempec_pacbio/ec_pacbio.spec -p asm -d .
ovlMerThreshold=503 ovlHashLibrary=2 ovlRefLibrary=1-1 ovlCheckLibrary=1
obtHashLibrary=1-1 obtRefLibrary=1-1 obtCheckLibrary=0
gridEnginePropagateHold="pBcR_asm" stopAfter=overlapper
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