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  • Dindel crash whilst parsing bam-sorted file

    Dear All,

    Does have anyone idea what might have cause this crash?
    Thanks.
    Michal

    -------
    dindel --analysis getCIGARindels --bamFile ./Post_Assembly/Temp/2007.02142B.normal.merged.out.bam --outputFile normal.sorted.bam --ref ./Reference_Indexed/Human36
    -------
    Reading BAM file: ./Post_Assembly/Temp/2007.02142B.normal.merged.out.bam
    Parsing indels from CIGAR strings...
    Number of reads read: 1000000
    Number of reads read: 2000000
    Number of reads read: 3000000
    Number of reads read: 4000000
    Number of reads read: 5000000
    Number of reads read: 6000000
    Number of reads read: 7000000
    Number of reads read: 8000000
    Number of reads read: 9000000
    Number of reads read: 10000000
    Number of reads read: 11000000
    Number of reads read: 12000000
    Number of reads read: 13000000
    Number of reads read: 14000000
    Number of reads read: 15000000
    Number of reads read: 16000000
    Number of reads read: 17000000
    Number of reads read: 18000000
    error: faidx error, len==0
    start: -88 end:
    error: faidx error, len==0
    start: -48 end:
    error: faidx error, len==0
    start: -4 end:
    Last edited by michalkovac; 11-23-2010, 08:28 AM.

  • #2
    It seems to be complaining about your faidx file. Check whether ./Reference_Indexed/Human36 is a fasta file and that ./Reference_Indexed/Human36.fai exists and it was made with "samtools faidx" or Picard.
    It looks as though something is wrong with the reference sequence specified with --ref

    Comment


    • #3
      Reference file is ok and indexed with SAM tools. Or alternatively, dindel makes it's own fai when absent.

      Comment


      • #4
        I am using dindel 1.01 and my command is

        Code:
        dindel --analysis getCIGARindels --bamFile  file.bam  --outputFile file.dindel --ref genome.fa

        Comment


        • #5
          I get same problem...The output file, sample.dindel_output.variants.txt, is empty...

          Comment


          • #6
            Forum search reveals:

            Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
            Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
            Projects: U87MG whole genome sequence [Website] [Paper]

            Comment


            • #7
              More information required

              Thank you for the important URL.
              in my Parsing indels from CIGAR strings...
              "error: faidx error, len==0" appears more than 300,000 times.
              And in the output files (sample.dindel_output.libraries.txt, sample.dindel_output.variants.txt), sample.dindel_output.variants.txt is empty.
              The URLs says "Also the faidx errors are apparently nothing to worry about.". So maybe other problem?
              Not final vcf file but "sample.dindel_output.variants.txt" created at the stage 1 is empty. (of course, final vcf is also empty)
              Is it normal? Actually I know my sequences have SNPs.

              Comment


              • #8
                the same problem with you

                Originally posted by prokagenomics View Post
                Thank you for the important URL.
                in my Parsing indels from CIGAR strings...
                "error: faidx error, len==0" appears more than 300,000 times.
                And in the output files (sample.dindel_output.libraries.txt, sample.dindel_output.variants.txt), sample.dindel_output.variants.txt is empty.
                The URLs says "Also the faidx errors are apparently nothing to worry about.". So maybe other problem?
                Not final vcf file but "sample.dindel_output.variants.txt" created at the stage 1 is empty. (of course, final vcf is also empty)
                Is it normal? Actually I know my sequences have SNPs.
                I have the same problem.
                Many errors like this:
                ----------------
                Wrote indels in CIGARS for target NR_027432:81795970-81828929 to file chr10.dindel_output2
                error: faidx error, len==0
                start: -20 end:
                error: faidx error, len==0
                start: -16 end:
                error: faidx error, len==0
                start: 1545 end:
                error: faidx error, len==0
                start: 2131 end:
                error: faidx error, len==0
                start: 2132 end:
                error: faidx error, len==0
                start: 1553 end:
                error: faidx error, len==0
                start: 1946 end:
                error: faidx error, len==0
                start: 633 end:
                --------------------------------

                and in the stage 1, the sample.dindel_output.variants.txt is empty.

                Did you fix this?

                Comment


                • #9
                  Empty sample.dindel_output.variants.txt file

                  I'm having the same problem of empty sample.dindel_output.variants.txt file.
                  Here is is my command:

                  Code:
                  dindel-1.01-linux-64bit --analysis getCIGARindels \
                                                  --bamFile $bamfile \
                                                  --outputFile $bamfile.dindel \
                                                  --ref $REF &
                  dindel-1.01-linux-64bit is the linux binary that I downloaded from http://www.sanger.ac.uk/resources/software/dindel/

                  I also get error outputs like the following:

                  error: faidx error, len==0
                  start: 242960712 end:
                  error: faidx error, len==0
                  start: 145017722 end:
                  error: faidx error, len==0
                  start: 244903563 end:
                  ...


                  Was anyone able to solve this problem?

                  Comment

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