Overlap prep job failed

[Medhat]

I am trying to do the example here

PacBio

specially this type "Correction using complementary data";

I used this commands

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

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?

[wikander]

Can you paste the contents of your pacbio.spec file?

[Medhat]

It is just simple

merSize=14

[cvargasc]

Hello,

I'm having the same issue.

Partitioning for hash: 210616671-210877666 ref: 1,210616670
HASH 210616671- 210785993 REFR 1- 210616670 STRINGS 169323 BASES 1000004712 JOB 1
HASH 210785994- 210877666 REFR 1- 210616670 STRINGS 91673 BASES 533324435 JOB 2
----------------------------------------END Tue Dec 2 21:16:07 2014 (55 seconds)
ERROR: Overlap prep job /gnmP04/Soryzae/RawandFilteredReads/Illumina/PE/CA//temppacbio/1-overlapper/long_reads_part 1 FAILED.
ERROR: Overlap prep job /gnmP04/Soryzae/RawandFilteredReads/Illumina/PE/CA//temppacbio/1-overlapper/long_reads_part 2 FAILED.

2 overlap partitioning jobs failed.

I have tried modifying the pacbio.spec file, the only line I'm keeping is merylMemory = 32000.

And the command I'm using is PBcR -length 500 -partitions 200 -libraryname pacbio -threads 20 -s pacbio.spec -fastq allreads.fastq illuminaPE.frg

Does anyone have any idea of what could be the issue?

Thanks in advance!

[cwisch88]

cvargasc,

I wanted to respond to his still unanswered question because I ran into this issue this week.

I discovered that there is an error file in the 1-overlapper directory ending with *.err. Inside it said that the binary sawriter was missing.

I suggest reading through any error files produced in that directory, if there is any mention of sawriter, you'll need to install blasr and perhaps the library it depends on hdf5.

After installing the PBcR stopped giving me that particular error.

Here's the thread that helped me:

http://sourceforge.net/p/wgs-assembler/mailman/message/33127830/