bfast localalign error

[kenietz]

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

[nilshomer]

I am sorry you are experience a problem. Could you try removing reads from your fastq until you have a small test case?

[kenietz]

Hi Nils,
im sorry to bother you with so many problems lately.

Update on my current problem with bfast align: I started it with -U option and like this the aligning start without complain like in my previous post. I only do not know what is the consequence of that action later. I mean how will affect the end result. Could you please explain why i could get such an error and what is the outcome of using -U?

Thank you for your time and help

[nilshomer]

It will just run slower, but you should get the same results. The error may result of malformed input in the fasta or fastq, hence why I was saying to try to reduce the fastq (or use the -s/-e in localalign) to isolate the problem. That would be helpful, as my guessing is not.