I am trying to do the example here
PacBio
specially this type "Correction using complementary data";
I used this commands
but it gives me this Error
Dumping 7550 fragments from library IID 2
/home/medhat/Downloads/sampleData//templambdaIll/1-overlapper/ovlprep.sh 2
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 25000 fragments from library IID 1
Dumping 0 fragments from library IID 2
----------------------------------------END CONCURRENT Mon Jul 7 11:48:04 2014 (0 seconds)
ERROR: Overlap prep job /home/medhat/Downloads/sampleData//templambdaIll/1-overlapper/long_reads_part 1 FAILED.
1 overlap partitioning jobs failed.
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@2
I used totally different machine and it gives me this error
Fragment correction job 0001 failed.
================================================================================
runCA failed.
----------------------------------------
Stack trace:
at /home/medhat/source/celera/wgs-8.2alpha/Linux-amd64/bin/runCA line 1568
main::caFailure('1 overlap jobs failed; remove /home/medhat/lambda-example/sam...', undef) called at /home/medhat/source/celera/wgs-8.2alpha/Linux-amd64/bin/runCA line 4327
main:verlapCorrection() called at /home/medhat/source/celera/wgs-8.2alpha/Linux-amd64/bin/runCA line 6476
----------------------------------------
Failure message:
1 overlap jobs failed; remove /home/medhat/lambda-example/sampleData/lambdaIll/3-overlapcorrection/frgcorr.sh to try again
----------------------------------------END Mon Jul 14 12:36:54 2014 (6 seconds)
Failed to execute /home/medhat/source/celera/wgs-8.2alpha/Linux-amd64/bin/runCA -s /home/medhat/lambda-example/sampleData//templambdaIll/lambdaIll.spec -p asm -d lambdaIll ovlRefBlockLength=100000000000 ovlRefBlockSize=0 useGrid=0 scriptOnGrid=0 unitigger=bogart ovlErrorRate=0.03 utgErrorRate=0.013 cgwErrorRate=0.1 cnsErrorRate=0.1 utgGraphErrorLimit=0 utgGraphErrorRate=0.013 utgMergeErrorLimit=0 utgMergeErrorRate=0.02 frgCorrBatchSize=100000 doOverlapBasedTrimming=1 obtErrorRate=0.03 obtErrorLimit=4.5 frgMinLen=605.993313521545 ovlMinLen=80 consensus=pbutgcns merSize=22 cnsMaxCoverage=1 cnsReuseUnitigs=1 sgePropagateHold="pBcR_asm" lambdaIll.longest25.frg
any idea?
PacBio
specially this type "Correction using complementary data";
I used this commands
Code:
java -jar convertFastaAndQualToFastq.jar pacbio.filtered_subreads.fasta > pacbio.filtered_subreads.fastq /bin/fastqToCA -libraryname illumina -technology illumina -type sanger -innie -reads illumina.fastq > illumina.frg /bin/PBcR -length 500 -partitions 200 -l lambdaIll -s pacbio.spec -fastq pacbio.filtered_subreads.fastq genomeSize=50000 illumina.frg
Dumping 7550 fragments from library IID 2
/home/medhat/Downloads/sampleData//templambdaIll/1-overlapper/ovlprep.sh 2
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 25000 fragments from library IID 1
Dumping 0 fragments from library IID 2
----------------------------------------END CONCURRENT Mon Jul 7 11:48:04 2014 (0 seconds)
ERROR: Overlap prep job /home/medhat/Downloads/sampleData//templambdaIll/1-overlapper/long_reads_part 1 FAILED.
1 overlap partitioning jobs failed.
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@2
I used totally different machine and it gives me this error
Fragment correction job 0001 failed.
================================================================================
runCA failed.
----------------------------------------
Stack trace:
at /home/medhat/source/celera/wgs-8.2alpha/Linux-amd64/bin/runCA line 1568
main::caFailure('1 overlap jobs failed; remove /home/medhat/lambda-example/sam...', undef) called at /home/medhat/source/celera/wgs-8.2alpha/Linux-amd64/bin/runCA line 4327
main:verlapCorrection() called at /home/medhat/source/celera/wgs-8.2alpha/Linux-amd64/bin/runCA line 6476
----------------------------------------
Failure message:
1 overlap jobs failed; remove /home/medhat/lambda-example/sampleData/lambdaIll/3-overlapcorrection/frgcorr.sh to try again
----------------------------------------END Mon Jul 14 12:36:54 2014 (6 seconds)
Failed to execute /home/medhat/source/celera/wgs-8.2alpha/Linux-amd64/bin/runCA -s /home/medhat/lambda-example/sampleData//templambdaIll/lambdaIll.spec -p asm -d lambdaIll ovlRefBlockLength=100000000000 ovlRefBlockSize=0 useGrid=0 scriptOnGrid=0 unitigger=bogart ovlErrorRate=0.03 utgErrorRate=0.013 cgwErrorRate=0.1 cnsErrorRate=0.1 utgGraphErrorLimit=0 utgGraphErrorRate=0.013 utgMergeErrorLimit=0 utgMergeErrorRate=0.02 frgCorrBatchSize=100000 doOverlapBasedTrimming=1 obtErrorRate=0.03 obtErrorLimit=4.5 frgMinLen=605.993313521545 ovlMinLen=80 consensus=pbutgcns merSize=22 cnsMaxCoverage=1 cnsReuseUnitigs=1 sgePropagateHold="pBcR_asm" lambdaIll.longest25.frg
any idea?
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