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  • sdvie
    Member
    • Jul 2010
    • 68

    bfast postprocess "AlignedEntryGetAlignment" error

    Dear all,

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

    Code:
    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
    Nils Homer
    • Nov 2008
    • 1283

    #2
    Originally posted by sdvie View Post
    Dear all,

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

    Code:
    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.

    Comment

    • sdvie
      Member
      • Jul 2010
      • 68

      #3
      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

      Comment

      • nilshomer
        Nils Homer
        • Nov 2008
        • 1283

        #4
        Excellent, thanks for the great insight.

        Comment

        • xiangwulu
          Member
          • Apr 2014
          • 18

          #5
          what does "avgMismatchQuality" mean?
          does it refer to something with the base quality of mismach base?

          Comment

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