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.
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.
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