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Old 04-20-2017, 05:12 AM   #1
mido1951
Senior Member
 
Location: Tunisia

Join Date: May 2014
Posts: 123
Default problem in PacBioToCA in correction of long reads

Hello,

I try to run PacBioToCA to correct long reads.

But here is the error.
Quote:
Quote:

###
### Reading options from 'spec_file.spec'
###

Warning: no frag files specified, assuming self-correction of pacbio sequences.
Running with 8 threads and 200 partitions
********* Starting correction...
CA: /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin
AMOS:/usr/local/genome/amos/bin
SMRTportal:/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin (blasr 1.3.1.142244)
Bowtie:/usr/local/genome/bin
******** Configuration Summary ********
cnsErrorRate = 0.25
gridEngineHoldOption = -hold_jid "WAIT_TAG"
utgErrorRate = 0.15
mhapLoadFactor = 12500
onlyContained = 0
gridEngineOutputOption = -j y -o
gridOptionsOverlapCorrection = -pe threads 1
asmObtErrorLimit = 4.5
gridOptionsCorrection = -pe threads 16 -l mem=2GB
gridOptionsFragmentCorrection = -pe threads 2
ovlCorrConcurrency = 4
submitToGrid = 0
maxUncorrectedGap = 1500
mhapVersion = 1.5b1
ovlRefBlockLength = 100000000000
blasr =
gridEngineArraySubmitID = $TASK_ID
ovlConcurrency = 8
merylThreads = 8
utgMergeErrorRate = 0.025
gridOptionsScript = -pe threads 16
asmCnsErrorRate = 0.1
gridOptionsOverlap = -pe threads 2
falconForce =
mhapPrecompute = 1
cleanup = 1
shortReads =
merCompression = 1
doOverlapBasedTrimming = 0
gridEngineJobID = JOB_ID
assembleCoverage = 25
asmMerSize = 22
genomeSize = 4.8m
cgwErrorRate = 0.25
gridEngineArrayName = ARRAY_NAME
merylMemory = 128000
libraryname = LIB
consensusConcurrency = 4
utgGraphErrorRate = 0.025
asmCgwErrorRate = 0.1
repeats =
useGrid = 0
gridEngineNameToJobIDCommand =
gridEngineSubmitCommand = qsub
asmObtErrorRate = 0.03
assemble = 1
ovlMemory = 251
ovlHashBits = 25
frgCorrBatchSize = 100000
frgMinLen = 64
batOptions = -RS -NS -CS
merOverlapperExtendBatchSize = 250000
asmOvlErrorRate = 0.03
longReads = 1
utgGraphErrorLimit = 0
specFile = spec_file.spec
pbcns = 0
partitions = 200
merSize = 14
merOverlapperSeedBatchSize = 500000
bowtie =
frgCorrOnGrid = 0
scriptOnGrid = 0
ovlErrorRate = 0.25
gridEngineArrayOption = -t ARRAY_JOBS
coverageCutoff = 0
frgCorrConcurrency = 2
ovlHashBlockLength = 20000000
gridOptionsConsensus = -pe threads 1
QV = 54.5
cnsMinFrags = 1000
merOverlapperThreads = 3
gridEngineSyncOption = -sync y
utgErrorLimit = 4.5
doUnitigSplitting = 0
cnsConcurrency = 4
samFOFN =
ovlStoreMemory = 8192
gridEngineTaskID = SGE_TASK_ID
length = 500
unitigger = bogart
maxCoverage = 40
stopAfter = overlapper
asmUtgErrorRate = 0.025
bankPath =
gridOptions = -A assembly
fastqFile = /projet/maiage/save/user/Bureau/WEcoli_raw.fastq
doFragmentCorrection = 1
merOverlapperExtendConcurrency = 3
merOverlapperSeedConcurrency = 3
asmOBT = 1
ovlCorrBatchSize = 100000
ovlCorrOnGrid = 0
sensitive = 0
mhap =
gridEngineNameOption = -cwd -N
assembleMinCoverage = 10
threads = 8
falconcns = 1
gridEnginePropagateCommand = qalter -hold_jid "WAIT_TAG"
shell = /bin/bash
ovlRefBlockSize = 50000000
asmCns = pbutgcns
gridOptionsMhap = -pe threads 2
utgMergeErrorLimit = 0
falconOptions = --max_n_read 200 --min_idt 0.70 --output_multi --local_match_count_threshold 2
frgCorrThreads = 2
ovlThreads = 8
****************
----------------------------------------START Thu Apr 20 13:47:24 2017
mkdir tempLIB
----------------------------------------END Thu Apr 20 13:47:24 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:47:24 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/fastqToCA -libraryname LIB -type sanger -technology none -feature doConsensusCorrection 1 -reads /projet/maiage/save/user/Bureau/WEcoli_raw.fastq > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.frg
----------------------------------------END Thu Apr 20 13:47:24 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:47:24 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d tempLIB stopAfter=initialStoreBuilding /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.frg
ENV: SGE_TASK_ID needs to be unset, done.
----------------------------------------START Thu Apr 20 13:47:24 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/asm.gkpStore.BUILDING -F /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.frg > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/asm.gkpStore.err 2>&1
----------------------------------------END Thu Apr 20 13:47:26 2017 (2 seconds)
numFrags = 8451
Stop requested after 'initialstorebuilding'.
----------------------------------------END Thu Apr 20 13:47:26 2017 (2 seconds)
Will be correcting PacBio library 1 with librarie[s] 1 - 1
----------------------------------------START Thu Apr 20 13:47:26 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -dumpfragments -invert -tabular -longestovermin 1 500 -longestlength 1 192 /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.gkpStore 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.seedlength |awk '{if (!(match($1, "UID") != 0 && length($1) == 3)) { print "frg uid "$1" isdeleted 1"; } }' > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.toerase.uid
----------------------------------------END Thu Apr 20 13:47:26 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:47:26 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper --edit /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.toerase.uid /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.gkpStore > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.toerase.out 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.toerase.err
----------------------------------------END Thu Apr 20 13:47:26 2017 (0 seconds)
Running with 6684.375X (for genome size 4.8m) of LIB sequences (32085 bp).
Correcting with 10887268X sequences (52258890 bp).
Warning: enabling MHAP overlapper to align long reads to long reads.
----------------------------------------START Thu Apr 20 13:47:26 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/jellyfish count -m 14 -s 120000000 -t 8 -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.mers /projet/maiage/save/user/Bureau/WEcoli_raw.fastq
----------------------------------------END Thu Apr 20 13:47:29 2017 (3 seconds)
----------------------------------------START Thu Apr 20 13:47:29 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/jellyfish histo -t 8 -f /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.mers > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.hist
----------------------------------------END Thu Apr 20 13:47:31 2017 (2 seconds)
----------------------------------------START Thu Apr 20 13:47:31 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/jellyfish dump -c -t -L 6 /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.mers |awk -v TOTAL=38698633 '{printf("%s\t%0.10f\t%d\t%d\n", $1, $2/TOTAL, $2, TOTAL)}' |sort -T . -rnk2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.ignore
----------------------------------------END Thu Apr 20 13:47:35 2017 (4 seconds)
----------------------------------------START Thu Apr 20 13:47:35 2017
rm /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.mers*
----------------------------------------END Thu Apr 20 13:47:35 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:47:35 2017
mkdir /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/1-overlapper
----------------------------------------END Thu Apr 20 13:47:35 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:47:35 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -dumpfragments -tabular asm.gkpStore |awk '{print $1"\t"$2}' > asm.eidToIID
----------------------------------------END Thu Apr 20 13:47:35 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:47:35 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -dumpfragments -tabular asm.gkpStore |awk '{print $2"\t"$10}' > asm.iidToLen
----------------------------------------END Thu Apr 20 13:47:35 2017 (0 seconds)
----------------------------------------START CONCURRENT Thu Apr 20 13:47:35 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/1-overlapper/ovlprep.sh 1
Scanning store to find libraries used and reads to dump.
Added 0 reads to maintain mate relationships.
Dumping 0 fragments from unknown library (version 1 has these)
Dumping 8451 fragments from library IID 1
----------------------------------------END CONCURRENT Thu Apr 20 13:48:39 2017 (64 seconds)
----------------------------------------START CONCURRENT Thu Apr 20 13:48:39 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/1-overlapper/overlap.sh 1
----------------------------------------END CONCURRENT Thu Apr 20 13:48:46 2017 (7 seconds)
----------------------------------------START Thu Apr 20 13:48:46 2017
rm -f 000001.ovls
----------------------------------------END Thu Apr 20 13:48:46 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:48:46 2017
rm -f *.dat
----------------------------------------END Thu Apr 20 13:48:46 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:48:46 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d . ovlMerThreshold= ovlHashLibrary=1 ovlRefLibrary=1-1 ovlCheckLibrary=1 obtHashLibrary=1-1 obtRefLibrary=1-1 obtCheckLibrary=0 gridEnginePropagateHold="pBcR_asm" stopAfter=overlapper
ENV: SGE_TASK_ID needs to be unset, done.
----------------------------------------START Thu Apr 20 13:48:47 2017
find -L /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./1-overlapper \( -name \*ovb.gz -or -name \*ovb \) -print > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.ovlStore.list
----------------------------------------END Thu Apr 20 13:48:47 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:48:47 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.ovlStore.BUILDING -g /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.gkpStore -M 8192 -L /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.ovlStore.list > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.ovlStore.err 2>&1
----------------------------------------END Thu Apr 20 13:48:47 2017 (0 seconds)
Stop requested after 'overlapper'.
----------------------------------------END Thu Apr 20 13:48:47 2017 (1 seconds)
----------------------------------------START Thu Apr 20 13:48:47 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runCorrection.sh
----------------------------------------END Thu Apr 20 13:48:48 2017 (1 seconds)
----------------------------------------START Thu Apr 20 13:48:48 2017
rm -rf asm.paired.ovlStore
----------------------------------------END Thu Apr 20 13:48:48 2017 (0 seconds)
----------------------------------------START CONCURRENT Thu Apr 20 13:48:48 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 1
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 2
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 3
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 4
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 5
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 6
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 7
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 8
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 9
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 10
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 11
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 12
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 13
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/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 90
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 91
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 92
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 93
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 94
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 95
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 96
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 97
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 98
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 99
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 100
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 101
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 102
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 103
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 104
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 105
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 106
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 107
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 108
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 109
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 110
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 111
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 112
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 113
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 114
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 115
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 116
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 117
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 118
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 119
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 120
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 121
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 122
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 123
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 124
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 125
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 126
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 127
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 128
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 129
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 130
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 131
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 132
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 133
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 134
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 135
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 136
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 137
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 138
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 139
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 140
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 141
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 142
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 143
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 144
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 145
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 146
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 147
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 148
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 149
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 150
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 151
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 152
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 153
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 154
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 155
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 156
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 157
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 158
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 159
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 160
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 161
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 162
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 163
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 164
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 165
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 166
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 167
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 168
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 169
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 170
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 171
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 172
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 173
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 174
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 175
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 176
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 177
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 178
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 179
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 180
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 181
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 182
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 183
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 184
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 185
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 186
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 187
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 188
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 189
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 190
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 191
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 192
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 193
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 194
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 195
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 196
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 197
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 198
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 199
/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 200
----------------------------------------END CONCURRENT Thu Apr 20 13:49:44 2017 (56 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
rm -rf core.*
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
cat `ls asm.[0-9]*.log | sort -T . -rnk1` > corrected.log
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
cat corrected.log |awk '{print $1}' |sort -T . |uniq -c |awk '{if ($1 > 1) print $2}' > asm.split.uid
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
cp asm.layout.err /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.correction.err
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
cp asm.layout.hist /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.correction.hist
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
cat `ls [0-9]*.fasta |grep trim |sort -T . -rnk1` > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.fasta
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
cat `ls [0-9]*.qual |grep trim | sort -T . -rnk1` > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.qual
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
cat `ls [0-9]*.fastq |grep trim | sort -T . -rnk1` > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.fastq
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/fastqToCA -libraryname LIB -technology pacbio-corrected -type sanger -reads /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.fastq > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.frg
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
ls: impossible d'accéder à /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/*sge.out*: Aucun fichier ou dossier de ce type
******** Correction Summary ********
----------------------------------------START Thu Apr 20 13:49:44 2017
rm -rf tempLIB/[0-9]*.*
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
rm -rf tempLIB/asm.[0-9]*.log
----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:44 2017
rm -rf tempLIB/asm.gkpStore
----------------------------------------END Thu Apr 20 13:49:45 2017 (1 seconds)
----------------------------------------START Thu Apr 20 13:49:45 2017
rm -rf tempLIB/asm.ovlStore
----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:45 2017
rm -rf tempLIB/asm.[0-9]*.lay
----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
********* Finished correcting 32085 bp (using 52258890 bp).
********* Assembling corrected sequences.
Assembling with average 8437 (min frag 3000) and using ovl is 100
----------------------------------------START Thu Apr 20 13:49:45 2017
ln -sf LIB.fastq LIB.u.fastq
----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:45 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/fastqSample -U -I LIB -O LIB.longest25 -c 25 -g 4.8m -max
Counting the number of reads in the input.
Found 13649 bases and 2 reads in 'LIB.u.fastq'
Sorting by length
Extracting 1 reads into LIB.longest25.u.fastq
----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:45 2017
mv LIB.longest25.u.fastq LIB.longest25.fastq
----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:45 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/fastqToCA -libraryname LIB -technology pacbio-corrected -type sanger -reads /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.longest25.fastq > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.longest25.frg
----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:45 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d LIB ovlRefBlockLength=100000000000 ovlRefBlockSize=0 useGrid=0 scriptOnGrid=0 unitigger=bogart ovlErrorRate=0.03 utgErrorRate=0.025 cgwErrorRate=0.1 cnsErrorRate=0.1 utgGraphErrorLimit=0 utgGraphErrorRate=0.025 utgMergeErrorLimit=0 utgMergeErrorRate=0.025 frgCorrBatchSize=100000 doOverlapBasedTrimming=1 obtErrorRate=0.03 obtErrorLimit=4.5 frgMinLen=3000 ovlMinLen=100 "batOptions=-RS -NS -CS" consensus=pbutgcns merSize=22 cnsMaxCoverage=1 cnsReuseUnitigs=1 gridEnginePropagateHold="pBcR_asm" LIB.longest25.frg
ENV: SGE_TASK_ID needs to be unset, done.
----------------------------------------START Thu Apr 20 13:49:45 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore.BUILDING -T -F /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB.longest25.frg > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore.err 2>&1
----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
numFrags = 1
----------------------------------------START Thu Apr 20 13:49:45 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/initialTrim \
-log /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.initialTrim.log \
-frg /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore \
> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.initialTrim.summary \
2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.initialTrim.err
----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:45 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/meryl -B -C -v -m 22 -memory 128000 -threads 8 -c 0 -L 2 -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore:chain -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0 > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/meryl.err 2>&1
----------------------------------------END Thu Apr 20 13:49:46 2017 (1 seconds)
----------------------------------------START Thu Apr 20 13:49:46 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/estimate-mer-threshold -m /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0 > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0.estMerThresh.out 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0.estMerThresh.err
----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:46 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/meryl -Dt -n 1048576 -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0 > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm.nmers.obt.fasta 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm.nmers.obt.fasta.err
----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:46 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/meryl -Dt -n 1048576 -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0 > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm.nmers.ovl.fasta 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm.nmers.ovl.fasta.err
----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
Reset OBT mer threshold from to 1048576.
Reset OVL mer threshold from to 1048576.
----------------------------------------START Thu Apr 20 13:49:46 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/overlap_partition \
-g /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore \
-bl 20000000 \
-bs 0 \
-rs 0 \
-rl 100000000000 \
-o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim-overlap \
> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim-overlap/overlap_partition.err 2>&1
----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
Created 0 overlap jobs. Last batch '', last job ''.
----------------------------------------START CONCURRENT Thu Apr 20 13:49:46 2017
----------------------------------------END CONCURRENT Thu Apr 20 13:49:46 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:46 2017
find -L /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim-overlap \( -name \*ovb.gz -or -name \*ovb \) -print > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.list
----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
----------------------------------------START Thu Apr 20 13:49:46 2017
/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild -obt -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.BUILDING -g /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore -M 8192 -L /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.list > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.err 2>&1
----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

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

at /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 1628.
main::caFailure("failed to build the obt store", "/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/L"...) called at /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 3819
main:verlapTrim() called at /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 6252

----------------------------------------
Last few lines of the relevant log file (/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.err):


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

failed to build the obt store

----------------------------------------END Thu Apr 20 13:49:46 2017 (1 seconds)
Failed to execute /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d LIB ovlRefBlockLength=100000000000 ovlRefBlockSize=0 useGrid=0 scriptOnGrid=0 unitigger=bogart ovlErrorRate=0.03 utgErrorRate=0.025 cgwErrorRate=0.1 cnsErrorRate=0.1 utgGraphErrorLimit=0 utgGraphErrorRate=0.025 utgMergeErrorLimit=0 utgMergeErrorRate=0.025 frgCorrBatchSize=100000 doOverlapBasedTrimming=1 obtErrorRate=0.03 obtErrorLimit=4.5 frgMinLen=3000 ovlMinLen=100 "batOptions=-RS -NS -CS" consensus=pbutgcns merSize=22 cnsMaxCoverage=1 cnsReuseUnitigs=1 gridEnginePropagateHold="pBcR_asm" LIB.longest25.frg
can you help me
thanks

Last edited by mido1951; 04-20-2017 at 07:26 AM.
mido1951 is offline   Reply With Quote
Old 04-20-2017, 07:28 AM   #2
mido1951
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Location: Tunisia

Join Date: May 2014
Posts: 123
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Problem resolved
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