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Re: [wgs-assembler-users] pacBioToCA: caFailure('can\'t set both ovlRefBlockSize and ovlRefBlockLength'
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From: Serge K. <ser...@gm...> - 2015-03-26 20:51:44
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Hi,
This is because the program sets the ovlRefBlockLength by default. Just remove the ovlRefBlockSize from your spec file (or add ovlRefBlockLength=0) and it should run.
Sergey
> On Mar 25, 2015, at 8:55 PM, Adrian Pelin <ape...@gm...> wrote:
>
> 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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