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Old 03-22-2017, 07:54 AM   #1
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Location: Germany

Join Date: Nov 2015
Posts: 4
Default 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:

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!


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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