Hi everyone,
I have been trying to get pacbioToCA to work for the past 3 weeks without luck. Every time it failed at the MerTrim stage.
To troubleshoot this, I download the example data set from the pacBioToCA wiki: http://sourceforge.net/apps/mediawik...o_RS_Sequences.
I followed very carefully to generate frg file, convert fasta to fastq. These were all fine. But when I did the error correct from command line: /home/zzong/bin/wgs-7.0/Linux-amd64/bin/pacBioToCA -length 500 -partitions 200 -l pacbio -t 16 -s pacbio.spec -fastq pacbio.filtered_subreads.fastq illumina.frg > run.out 2>&1
I got the merTrim error again. I suspect it has something to do with the spec file. However, it was downloaded from the sampleData set. Are there some parameters need to be adjusted? Could someone help to have a look what went wrong and help me out? The error messages in the run.out file are as follow:
Many thanks in advance!
Stuart
#######################
pacbio.spc
# 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
ovlHashBits = 24
ovlThreads = 2
ovlHashBlockLength = 20000000
ovlRefBlockSize = 50000000
frgCorrThreads = 2
frgCorrBatchSize = 100000
ovlCorrBatchSize = 100000
ovlConcurrency = 6
cnsConcurrency = 16
frgCorrConcurrency = 8
ovlCorrConcurrency = 16
cnsConcurrency = 16
Error messages:
###############################################
Running with 16 threads and 200 partitions
Starting correction...
CA: /home/zzong/bin/wgs-7.0/Linux-amd64/bin
AMOS:/home/zzong/bin/amos-3.1.0/src/Bank
----------------------------------------START Sun Mar 31 19:40:43 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/fastqToCA -libraryname PacBio -type sanger -innie -technology pacbio -reads /home/zzong/project/chlamy/sampleData/pacbio.filtered_subreads.fastq > /home/zzong/project/chlamy/sampleData//pacbio.frg
----------------------------------------END Sun Mar 31 19:40:43 2013 (0 seconds)
----------------------------------------START Sun Mar 31 19:40:43 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio sge=" -sync y" sgePropagateHold=corAsm stopAfter=initialStoreBuilding illumina.frg /home/zzong/project/chlamy/sampleData//pacbio.frg
----------------------------------------START Sun Mar 31 19:40:43 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/gatekeeper -o /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore.BUILDING -T -F /home/zzong/project/chlamy/sampleData/illumina.frg /home/zzong/project/chlamy/sampleData//pacbio.frg > /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore.err 2>&1
----------------------------------------END Sun Mar 31 19:40:45 2013 (2 seconds)
numFrags = 28747
Stop requested after 'initialstorebuilding'.
----------------------------------------END Sun Mar 31 19:40:45 2013 (2 seconds)
----------------------------------------START Sun Mar 31 19:40:45 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio ovlHashLibrary=2 ovlRefLibrary=1-1 obtHashLibrary=1-1 obtRefLibrary=1-1 sge=" -sync y" sgePropagateHold=corAsm stopAfter=overlapper
----------------------------------------START Sun Mar 31 19:40:45 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/meryl -B -C -v -m 14 -memory 128000 -threads 16 -c 0 -L 2 -s /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore:chain -o /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/meryl.err 2>&1
----------------------------------------END Sun Mar 31 19:40:47 2013 (2 seconds)
----------------------------------------START Sun Mar 31 19:40:47 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/estimate-mer-threshold -g /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore:chain -m /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0.estMerThresh.out 2> /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0.estMerThresh.err
----------------------------------------END Sun Mar 31 19:40:47 2013 (0 seconds)
----------------------------------------START Sun Mar 31 19:40:47 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/meryl -Dt -n 62 -s /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.ovl.fasta 2> /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.ovl.fasta.err
----------------------------------------END Sun Mar 31 19:40:47 2013 (0 seconds)
----------------------------------------START Sun Mar 31 19:40:47 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/meryl -Dt -n 62 -s /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.obt.fasta 2> /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.obt.fasta.err
----------------------------------------END Sun Mar 31 19:40:48 2013 (1 seconds)
Reset OBT mer threshold from auto to 62.
Reset OVL mer threshold from auto to 62.
----------------------------------------START CONCURRENT Sun Mar 31 19:40:48 2013
/home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim/mertrim.sh 1 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim/asm.0001.err 2>&1
----------------------------------------END CONCURRENT Sun Mar 31 19:40:48 2013 (0 seconds)
================================================================================
runCA failed.
----------------------------------------
Stack trace:
at /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA line 1237.
main::caFailure('merTrim failed. See *.err in /home/zzong/project/chlamy/samp...', undef) called at /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA line 2794
main::merTrim() called at /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA line 5875
----------------------------------------
Failure message:
merTrim failed. See *.err in /home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim
----------------------------------------END Sun Mar 31 19:40:48 2013 (3 seconds)
Failed to execute /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio ovlHashLibrary=2 ovlRefLibrary=1-1 obtHashLibrary=1-1 obtRefLibrary=1-1 sge=" -sync y" sgePropagateHold=corAsm stopAfter=overlapper
I have been trying to get pacbioToCA to work for the past 3 weeks without luck. Every time it failed at the MerTrim stage.
To troubleshoot this, I download the example data set from the pacBioToCA wiki: http://sourceforge.net/apps/mediawik...o_RS_Sequences.
I followed very carefully to generate frg file, convert fasta to fastq. These were all fine. But when I did the error correct from command line: /home/zzong/bin/wgs-7.0/Linux-amd64/bin/pacBioToCA -length 500 -partitions 200 -l pacbio -t 16 -s pacbio.spec -fastq pacbio.filtered_subreads.fastq illumina.frg > run.out 2>&1
I got the merTrim error again. I suspect it has something to do with the spec file. However, it was downloaded from the sampleData set. Are there some parameters need to be adjusted? Could someone help to have a look what went wrong and help me out? The error messages in the run.out file are as follow:
Many thanks in advance!
Stuart
#######################
pacbio.spc
# 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
ovlHashBits = 24
ovlThreads = 2
ovlHashBlockLength = 20000000
ovlRefBlockSize = 50000000
frgCorrThreads = 2
frgCorrBatchSize = 100000
ovlCorrBatchSize = 100000
ovlConcurrency = 6
cnsConcurrency = 16
frgCorrConcurrency = 8
ovlCorrConcurrency = 16
cnsConcurrency = 16
Error messages:
###############################################
Running with 16 threads and 200 partitions
Starting correction...
CA: /home/zzong/bin/wgs-7.0/Linux-amd64/bin
AMOS:/home/zzong/bin/amos-3.1.0/src/Bank
----------------------------------------START Sun Mar 31 19:40:43 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/fastqToCA -libraryname PacBio -type sanger -innie -technology pacbio -reads /home/zzong/project/chlamy/sampleData/pacbio.filtered_subreads.fastq > /home/zzong/project/chlamy/sampleData//pacbio.frg
----------------------------------------END Sun Mar 31 19:40:43 2013 (0 seconds)
----------------------------------------START Sun Mar 31 19:40:43 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio sge=" -sync y" sgePropagateHold=corAsm stopAfter=initialStoreBuilding illumina.frg /home/zzong/project/chlamy/sampleData//pacbio.frg
----------------------------------------START Sun Mar 31 19:40:43 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/gatekeeper -o /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore.BUILDING -T -F /home/zzong/project/chlamy/sampleData/illumina.frg /home/zzong/project/chlamy/sampleData//pacbio.frg > /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore.err 2>&1
----------------------------------------END Sun Mar 31 19:40:45 2013 (2 seconds)
numFrags = 28747
Stop requested after 'initialstorebuilding'.
----------------------------------------END Sun Mar 31 19:40:45 2013 (2 seconds)
----------------------------------------START Sun Mar 31 19:40:45 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio ovlHashLibrary=2 ovlRefLibrary=1-1 obtHashLibrary=1-1 obtRefLibrary=1-1 sge=" -sync y" sgePropagateHold=corAsm stopAfter=overlapper
----------------------------------------START Sun Mar 31 19:40:45 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/meryl -B -C -v -m 14 -memory 128000 -threads 16 -c 0 -L 2 -s /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore:chain -o /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/meryl.err 2>&1
----------------------------------------END Sun Mar 31 19:40:47 2013 (2 seconds)
----------------------------------------START Sun Mar 31 19:40:47 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/estimate-mer-threshold -g /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore:chain -m /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0.estMerThresh.out 2> /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0.estMerThresh.err
----------------------------------------END Sun Mar 31 19:40:47 2013 (0 seconds)
----------------------------------------START Sun Mar 31 19:40:47 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/meryl -Dt -n 62 -s /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.ovl.fasta 2> /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.ovl.fasta.err
----------------------------------------END Sun Mar 31 19:40:47 2013 (0 seconds)
----------------------------------------START Sun Mar 31 19:40:47 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/meryl -Dt -n 62 -s /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.obt.fasta 2> /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.obt.fasta.err
----------------------------------------END Sun Mar 31 19:40:48 2013 (1 seconds)
Reset OBT mer threshold from auto to 62.
Reset OVL mer threshold from auto to 62.
----------------------------------------START CONCURRENT Sun Mar 31 19:40:48 2013
/home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim/mertrim.sh 1 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim/asm.0001.err 2>&1
----------------------------------------END CONCURRENT Sun Mar 31 19:40:48 2013 (0 seconds)
================================================================================
runCA failed.
----------------------------------------
Stack trace:
at /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA line 1237.
main::caFailure('merTrim failed. See *.err in /home/zzong/project/chlamy/samp...', undef) called at /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA line 2794
main::merTrim() called at /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA line 5875
----------------------------------------
Failure message:
merTrim failed. See *.err in /home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim
----------------------------------------END Sun Mar 31 19:40:48 2013 (3 seconds)
Failed to execute /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio ovlHashLibrary=2 ovlRefLibrary=1-1 obtHashLibrary=1-1 obtRefLibrary=1-1 sge=" -sync y" sgePropagateHold=corAsm stopAfter=overlapper
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