Hi guys,
i am using bfast 0.7a to align SOLID PE data and got that error at bfast localalign:
-- command used: bfast localalign -f hg19.fa -m reads.bmf -A 1 -n 8 > reads.baf
**** Input arguments look good! *****
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ~/Work_drive/Genomes/human/UCSC/BFAST_INDEX_CS/hg19.fa
matchFileName: HGC_27.fastq.bmf
scoringMatrixFileName: [Not Using]
ungapped: [Not Using]
unconstrained: [Not Using]
space: [Color Space]
startReadNum: 1
endReadNum: 2147483647
offsetLength: 20
maxNumMatches: 384
avgMismatchQuality: 10
numThreads: 8
queueLength: 25000
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from /home/domine/Work_drive/Genomes/human/UCSC/BFAST_INDEX_CS/hg19.fa.nt.brg.
In total read 25 contigs for a total of 3095693983 bases
************************************************************
************************************************************
Reading match file from HGC_27.fastq.bmf.
************************************************************
Performing alignment...
Reads processed: 0************************************************************
In function "AlignColorSpaceGappedConstrained": Fatal Error[OutOfRange]. Message: read and reference did not match.
***** Exiting due to errors *****
-----------------------------------------------------------------------
I have four fastq files and all of them throw an error.
I checked the threads around and saw that it might be due to building the NT and CS brg files with different versions of BFAST but i used 0.7a for both. And the same version for building the CS indexes.
I converted the solid reads to fastq with the solid2fastq file provided by bfast 0.7a as well. like this:
solid2fastq readF3.csfasta readsF5-P2.csfasta readF3.qual readsF5-P2.qual.
Have no idea what the problem could be now. Please help!!
Thank you
i am using bfast 0.7a to align SOLID PE data and got that error at bfast localalign:
-- command used: bfast localalign -f hg19.fa -m reads.bmf -A 1 -n 8 > reads.baf
**** Input arguments look good! *****
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ~/Work_drive/Genomes/human/UCSC/BFAST_INDEX_CS/hg19.fa
matchFileName: HGC_27.fastq.bmf
scoringMatrixFileName: [Not Using]
ungapped: [Not Using]
unconstrained: [Not Using]
space: [Color Space]
startReadNum: 1
endReadNum: 2147483647
offsetLength: 20
maxNumMatches: 384
avgMismatchQuality: 10
numThreads: 8
queueLength: 25000
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from /home/domine/Work_drive/Genomes/human/UCSC/BFAST_INDEX_CS/hg19.fa.nt.brg.
In total read 25 contigs for a total of 3095693983 bases
************************************************************
************************************************************
Reading match file from HGC_27.fastq.bmf.
************************************************************
Performing alignment...
Reads processed: 0************************************************************
In function "AlignColorSpaceGappedConstrained": Fatal Error[OutOfRange]. Message: read and reference did not match.
***** Exiting due to errors *****
-----------------------------------------------------------------------
I have four fastq files and all of them throw an error.
I checked the threads around and saw that it might be due to building the NT and CS brg files with different versions of BFAST but i used 0.7a for both. And the same version for building the CS indexes.
I converted the solid reads to fastq with the solid2fastq file provided by bfast 0.7a as well. like this:
solid2fastq readF3.csfasta readsF5-P2.csfasta readF3.qual readsF5-P2.qual.
Have no idea what the problem could be now. Please help!!
Thank you
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