From: Paul C. <pca...@gm...> - 2012-10-19 20:01:40
|
Hi I'm trying for the first time to assemble Illumina fastq reads. After running runCA 7.0 with: runCA -d cabogout -p SRR073769.uniq.bowtie.unmap SRR073769.uniq.bowtie.unmap.frg I got this output: ----------------------------------------START Fri Oct 19 15:54:42 2012 /Users/pgc92/Public/usr/local/wgs-7.0/Darwin-amd64/bin/gatekeeper -o /Users/pgc92/vdiscovery/analysis/Prensner2011/GSM618509/cabogout/SRR073769.uniq.bowtie.unmap.gkpStore.BUILDING -T -F /Users/pgc92/vdiscovery/analysis/Prensner2011/GSM618509/SRR073769.uniq.bowtie.unmap.frg > /Users/pgc92/vdiscovery/analysis/Prensner2011/GSM618509/cabogout/SRR073769.uniq.bowtie.unmap.gkpStore.err 2>&1 ----------------------------------------END Fri Oct 19 15:54:46 2012 (4 seconds) numFrags = 0 ================================================================================ runCA failed. ---------------------------------------- Stack trace: at /Users/pgc92/Public/usr/local/wgs/Darwin-i386/bin/runCA line 1237 main::caFailure('gatekeeper failed to add fragments', '/Users/pgc92/vdiscovery/analysis/Prensner2011/GSM618509/cabog...') called at /Users/pgc92/Public/usr/local/wgs/Darwin-i386/bin/runCA line 1698 main::preoverlap('/Users/pgc92/vdiscovery/analysis/Prensner2011/GSM618509/SRR07...') called at /Users/pgc92/Public/usr/local/wgs/Darwin-i386/bin/runCA line 5874 ---------------------------------------- Last few lines of the relevant log file (/Users/pgc92/vdiscovery/analysis/Prensner2011/GSM618509/cabogout/SRR073769.uniq.bowtie.unmap.gkpStore.err): Starting file '/Users/pgc92/vdiscovery/analysis/Prensner2011/GSM618509/SRR073769.uniq.bowtie.unmap.frg'. Processing SINGLE-ENDED SANGER QV encoding reads from: '/Users/pgc92/vdiscovery/analysis/Prensner2011/GSM618509/SRR073769.uniq.bowtie.unmap.fq' GKP finished with no alerts or errors. ---------------------------------------- Failure message: gatekeeper failed to add fragments What am I doing wrong? My fastq file contains ~1 million 45 bp reads with sanger quality values. Here is head output of the fastq file (57989) $ head SRR073769.uniq.bowtie.unmap.fq @SRR073769.109 PATHBIO-SOLEXA2:2:1:3:1029 length=45 CTGCCCAGGCATAGTTCACCATCTTTCGGGTCCTAACACGTGCGC +SRR073769.109 PATHBIO-SOLEXA2:2:1:3:1029 length=45 @@?@>@>@7@?9==@B@;@@@29>@6>3950:467>######### @SRR073769.111 PATHBIO-SOLEXA2:2:1:3:1362 length=45 TGGTTAGTTTCTTCTCCTCCGCTGACTAATATGCTTAAATTCAGA +SRR073769.111 PATHBIO-SOLEXA2:2:1:3:1362 length=45 CCCCCCC@CCCCCBCCBCCA@ABBCBBBCCBB8AB?6@ACB;?97 @SRR073769.113 PATHBIO-SOLEXA2:2:1:3:1458 length=45 GATCCACGGGGGCCGACCCGGTGACCCGGTTACCCGCCAGGTCCT Here is the output of the FRG file: (57990) $ cat *frg {VER ver:2 } {LIB act:A acc:SRR073769.uniq.bowtie.unmap ori:U mea:0.000 std:0.000 src: . nft:16 fea: forceBOGunitigger=1 isNotRandom=0 doNotTrustHomopolymerRuns=0 doTrim_initialNone=0 doTrim_initialMerBased=1 doTrim_initialFlowBased=0 doTrim_initialQualityBased=0 doRemoveDuplicateReads=1 doTrim_finalLargestCovered=1 doTrim_finalEvidenceBased=0 doRemoveSpurReads=1 doRemoveChimericReads=1 doConsensusCorrection=0 fastqQualityValues=sanger fastqOrientation=innie fastqReads=/Users/pgc92/vdiscovery/analysis/Prensner2011/GSM618509/SRR073769.uniq.bowtie.unmap.fq . } {VER ver:1 } Thank you, Paul Paul Cantalupo University of Pittsburgh |