bfast postprocess "AlignedEntryGetAlignment" error

[sdvie]

Dear all,

unexpectedly, I am getting the following error when trying to run bfast postprocess (alignment of 95 bp Illumina paired-end reads):

bfast+bwa-0.6.4e/bin/bfast postprocess -i t_8.baf -f hg19_indices/hg19.fa -a 3 -z -A 0 -R -O 1 -n 4 -U > t_8_alternative.sam
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /projects/bg/genomed/data/hg19_indices_ucsc/hg19.fa. 
Validating alignFileName t_8.baf. 
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode:			[ExecuteProgram]
fastaFileName:			/projects/bg/genomed/data/hg19_indices_ucsc/hg19.fa
alignFileName:			t_8.baf
algorithm:			[Best Score]
space:				[NT Space]
unpaired:			[Using]
reversePaired:			[Not Using]
avgMismatchQuality:		10
scoringMatrixFileName:		[Not Using]
randomBest:			[Not Using]
minMappingQuality:		-2147483648
minNormalizedScore:		-2147483648
pairingStandardDeviation:	2.000000
gappedPairingRescue		[Not Using]
numThreads:			4
queueLength:			50000
outputFormat:			[SAM]
outputID:			[Not Using]
RGFileName:			[Not Using]
timing:				[Not Using]
************************************************************
************************************************************
Reading in reference genome from /projects/bg/genomed/data/hg19_indices_ucsc/hg19.fa.nt.brg.
In total read 93 contigs for a total of 3137161264 bases
************************************************************
Postprocessing...
************************************************************
In function "AlignedEntryGetAlignment": Fatal Error[OutOfRange]. Message: Could not get reference sequence.
 ***** Exiting due to errors *****
************************************************************

I do not know what to make of this error - I ran a lot of analysis with the same reference sequence (in the same folder).

Suggestions are very much appreciated.

thanks and cheers,
Sophia

[nilshomer]

Dear all,

unexpectedly, I am getting the following error when trying to run bfast postprocess (alignment of 95 bp Illumina paired-end reads):

bfast+bwa-0.6.4e/bin/bfast postprocess -i t_8.baf -f hg19_indices/hg19.fa -a 3 -z -A 0 -R -O 1 -n 4 -U > t_8_alternative.sam
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /projects/bg/genomed/data/hg19_indices_ucsc/hg19.fa. 
Validating alignFileName t_8.baf. 
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode:			[ExecuteProgram]
fastaFileName:			/projects/bg/genomed/data/hg19_indices_ucsc/hg19.fa
alignFileName:			t_8.baf
algorithm:			[Best Score]
space:				[NT Space]
unpaired:			[Using]
reversePaired:			[Not Using]
avgMismatchQuality:		10
scoringMatrixFileName:		[Not Using]
randomBest:			[Not Using]
minMappingQuality:		-2147483648
minNormalizedScore:		-2147483648
pairingStandardDeviation:	2.000000
gappedPairingRescue		[Not Using]
numThreads:			4
queueLength:			50000
outputFormat:			[SAM]
outputID:			[Not Using]
RGFileName:			[Not Using]
timing:				[Not Using]
************************************************************
************************************************************
Reading in reference genome from /projects/bg/genomed/data/hg19_indices_ucsc/hg19.fa.nt.brg.
In total read 93 contigs for a total of 3137161264 bases
************************************************************
Postprocessing...
************************************************************
In function "AlignedEntryGetAlignment": Fatal Error[OutOfRange]. Message: Could not get reference sequence.
 ***** Exiting due to errors *****
************************************************************

I do not know what to make of this error - I ran a lot of analysis with the same reference sequence (in the same folder).

Suggestions are very much appreciated.

thanks and cheers,
Sophia

Please submit a test case to the bfast mailing list.

[sdvie]

Dear all and Nils,

when preparing the test set, I realized that the reference genome used for bfast postprocess was not the same I had used for alignment after all. (Too many editions of the hg19 around!) That is what caused the error.
However, as so often, to post the problem helped me to solve it .

Sorry for the confusion!

cheers,
Sophia

[nilshomer]

Excellent, thanks for the great insight.

[xiangwulu]

what does "avgMismatchQuality" mean?
does it refer to something with the base quality of mismach base?