Re: [wgs-assembler-users] gatekeeper failed to add fragments

[Walenz, B. <bw...@jc...>]

Hi, Paul-

The default minimum allowed read length is 64 bases, and so gatekeeper threw out all your reads.  Our error reporting on fastq inputs isn't terribly great, I'm afraid.  You can change the minimum with frgMinLen=40 on the command line.  The minimum overlap length is 40, an unless you've got great coverage, you might want to drop it as well (ovlMinLen).

The CA7 release is rather old, and we're suggesting people start using the 'unstable' version from CVS.

b
--
Brian Walenz
Senior Software Engineer
J. Craig Venter Institute


________________________________________
From: Paul Cantalupo [pca...@gm...]
Sent: Friday, October 19, 2012 4:01 PM
To: wgs-assembler-users
Subject: [wgs-assembler-users] gatekeeper failed to add fragments

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