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  • Pindel configuration file errors

    Hi there,

    I'm using Pindel, my configuration file looks like this:

    Sample_Barke.bam 400 Barke
    Sample_Bowman.bam 350 Bowman
    Sample_Bulbosum.bam 250 Bulbosum
    Sample_FT11.bam 300 FT11
    Sample_Igri.bam 300 Igri
    Sample_Morex.bam 300 Morex
    Sample_Pubiflorum.bam 200 Pubiflorum
    But when I run Pindel I get the following message:

    Code:
    pindel -f /data/filer/seq_shared/mascher/barley_pseudomolecules_150823/150823_barley_pseudomolecules_parts.fasta -i ../PINDEL/sampleBarleyPindel.cfg -c ALL -o ../PINDEL/pindelBarley -T 16
    Initializing parameters...
    Pindel version 0.2.5b9, 20160729.
    Loading reference genome ...
    Loading reference genome done.
    Could not find any samples in the sample file '../PINDEL/sampleBarleyPindel.cfg'. Please run Pindel again with a config-file of the specified type (format 'A.bam       <insert-size>   sample_label)
    any idea what I've been missing? Thank you, have a nice day!

    C.

    PS: I have also tried with absolute path in the command line, and with absolute path in the configuration file, but in both cases, it gave me the same error message

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