Hi,
I am trying to map exome data using bfast. I received *.sam files from our collaborates. Here's a summary of my method:
1. Converted *.sam to *.fastq using PICARD
2. Converted hg19.fa to color space - hg19.fa.cs.brg
3. Created index for reference - hg19.fa.cs.1.1.bif
4. Search indexes successful - *.bmf
5. Perform local alignment - gave me an error! Thanks to Seqanswers forums, I realized that I have to convert reference to nucleotide space as well. So, now I have hg19.fa.nt.brg
6. Tried to run local alignment again.....but got "AlignColorSpaceGappedConstrained" error!!!
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName chr_all.fa.
Validating matchFileName03C14605A_bfastMatches_hg19.bmf.
**** Input arguments look good! *****
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: chr_all.fa
matchFileName: 03C14605A_bfastMatches_hg19.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: 10000
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from chr_all.fa.nt.brg.
In total read 25 contigs for a total of 3095693983 bases
************************************************************
************************************************************
Reading match file from 03C14605A_bfastMatches_hg19.bmf.
************************************************************
Performing alignment...
Reads processed: 0************************************************************
In function "AlignColorSpaceGappedConstrained": Fatal Error[OutOfRange]. Message: read and reference did not match.
***** Exiting due to errors *****
************************************************************
Thank you in advance for your help.
Nimmi
I am trying to map exome data using bfast. I received *.sam files from our collaborates. Here's a summary of my method:
1. Converted *.sam to *.fastq using PICARD
2. Converted hg19.fa to color space - hg19.fa.cs.brg
3. Created index for reference - hg19.fa.cs.1.1.bif
4. Search indexes successful - *.bmf
5. Perform local alignment - gave me an error! Thanks to Seqanswers forums, I realized that I have to convert reference to nucleotide space as well. So, now I have hg19.fa.nt.brg
6. Tried to run local alignment again.....but got "AlignColorSpaceGappedConstrained" error!!!
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName chr_all.fa.
Validating matchFileName03C14605A_bfastMatches_hg19.bmf.
**** Input arguments look good! *****
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: chr_all.fa
matchFileName: 03C14605A_bfastMatches_hg19.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: 10000
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from chr_all.fa.nt.brg.
In total read 25 contigs for a total of 3095693983 bases
************************************************************
************************************************************
Reading match file from 03C14605A_bfastMatches_hg19.bmf.
************************************************************
Performing alignment...
Reads processed: 0************************************************************
In function "AlignColorSpaceGappedConstrained": Fatal Error[OutOfRange]. Message: read and reference did not match.
***** Exiting due to errors *****
************************************************************
Thank you in advance for your help.
Nimmi
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