BFAST localalign SOLiD data

[mnfuser]

Hi all, I am using BFAST to align SOLiD PE data.

I had the following error:

************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /state/partition1/genome/bfast/ucsc.hg19.fasta.
Validating matchFileName/share/GAMES/data/test20120501/solid0121_20100616_PEcllSureSelect_CLL_11.matched.bmf.
**** Input arguments look good! *****
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: /state/partition1/genome/bfast/ucsc.hg19.fasta
matchFileName: /share/GAMES/data/test20120501/solid0121_20100616_PEcllSureSelect_CLL_11.matched.bmf
scoringMatrixFileName: [Not Using]
ungapped: [Not Using]
unconstrained: [Not Using]
space: [Color Space]
startReadNum: 1
endReadNum: 2147483647
offsetLength: 20
maxNumMatches: 384
avgMismatchQuality: 10
numThreads: 1
queueLength: 25000
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from /state/partition1/genome/bfast/ucsc.hg19.fasta.nt.brg.
In total read 93 contigs for a total of 3137161264 bases
************************************************************
************************************************************
Reading match file from /share/GAMES/data/test20120501/solid0121_20100616_PEcllSureSelect_CLL_11.matched.bmf.
************************************************************
Performing alignment...
Reads processed: 0************************************************************

In function "AlignColorSpaceGappedConstrained": Fatal Error[OutOfRange]. Message: read and reference did not match.


Before alignment I built references with fast2brg in nt and cs. I created the masks and the indexes as mentioned in the manual (SOLiD section). I matched the .fastq file (obtained by solid2fastq, 2 .csfasta files + 2 .qual files) with the references. I got a 3.5 Gb .bmf file. When I started the local alignement I got an error as showed above.

What am I doing wrong? I hope anybody could help me..

Many thanks.

[nilshomer]

What where your match commands?

[mnfuser]

What where your match commands?

i) Indexes creation using 10 masks (as in BFAST manual):

$BFASTDIR/bfast/bfast index -n 8 -f $REFERENCEDIR/$REFERENCEFILE -m $MASK<1:10> -w 14 -i 7 -A 1

10 .bif files created successfully (13 Gb each)

ii) Matching step

$BFASTDIR/bfast/bfast match -f $REFERENCEDIR/$REFERENCEFILE -A 1 -r $OUTDIR/$READSFILE.fastq > $OUTDIR/$READSFILE.matched.bmf

REFERENCEFILE=ucsc.hg19.fa
READSFILE=solid0121_20100616_PEcllSureSelect_CLL_11 (obtained by running sold2fastq with .csfasta F3 and F5 files and 2 related .qual files)

Anything wrong?

Thanks

[nilshomer]

I would take a look at the bfast+bwa branch for paired ends. To debug, I would need a small test case.

[mnfuser]

I'm doing localalign with -U option and it's working. I will take a look at the bwaaln and related PE pipe to compare results.

I'm also reporting that while testing reads subsets with -s/-e in localalign, I got good results for such debug intervals. Error rised when localalign worked on the entire dataset, at the beginning of the computation (0 reads processed. I tested the interval 1:3000 and it worked).
I dont want to bother you more.

Let me know what you think about..


Thank for your interest

Cu,
Marco

[mnfuser]

The postprocess step, after alignment with -U option (it worked fine, I guess, and outputted a 4.5 Gb .baf file), gave me a segmentation fault error.

See below err message:

************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /state/partition1/genome/bfast/ucsc.hg19.fasta.
Validating alignFileName /share/GAMES/data/test20120501/solid0121_20100616_PEcllSureSelect_CLL_11.matched.bmf.aln.baf.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: /state/partition1/genome/bfast/ucsc.hg19.fasta
alignFileName: /share/GAMES/data/test20120501/solid0121_20100616_PEcllSureSelect_CLL_11.matched.bmf.aln.baf
algorithm: [Best Score]
space: [Color Space]
strandedness: [Opposite strand]
positioning: [Read one first]
pairing: [Paired End]
avgMismatchQuality: 10
scoringMatrixFileName: [Not Using]
randomBest: [Not Using]
minMappingQuality: -2147483648
minNormalizedScore: -2147483648
insertSizeAvg: 0.000000
insertSizeStdDev: 0.000000
numThreads: 8
queueLength: 100000
outputFormat: [SAM]
outputID: [Not Using]
RGFileName: [Not Using]
baseQualityType: [MAQ-style]
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from /state/partition1/genome/bfast/ucsc.hg19.fasta.nt.brg.
In total read 93 contigs for a total of 3137161264 bases
************************************************************
Postprocessing...
************************************************************
Estimating paired end distance...
Found only 0 distances to infer the insert size distribution
************************************************************

In function "GetPEDBins": Warning[OutOfRange]. Variable/Value: b->numDistances.
Message: Not enough distances to infer insert size distribution.
***** Warning *****
************************************************************
/opt/torque/mom_priv/jobs/878.deepseq.unife.it.SC: line 30: 28843 Segmentation fault $BFASTDIR/bfast/bfast postprocess -n 8 -f $REFERENCEDIR/$REFERENCEFILE -i $OUTDIR/$ALNFILE.baf -A 1 -Y 0 > $OUTDIR/$ALNFILE.sam

[nilshomer]

Very interesting, can you create a small test case to debug?

[mnfuser]

Hi, I ran bfast+BWA on centOS cluster, segmentation foult again (in index creation). It ran fine on my debian laptop. Any issues related to centOS?

Thank

[nilshomer]

I am sorry, there is not enough information to debug.