Pindel configuration file seems not working
Hi there,
I'm using Pindel, my configuration file look 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!
C.
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Did you try running it with absolute paths, probably its a path error since you might be in a different folder? Something like /data/filer/seq_shared/mascher/PINDEL/sampleBarleyPindel.cfg
Thank you for the idea but it doesn't work either, I have the same error message. Any other idea?
:)
C.
PS: I have also tried with path into the configuration file and it doesn't work either... :(
Did you use a tab or a space in the config file? Usually its a space, looks like you are using a tab
Ah yes, it was that! Thank you very much!
Have a nice day :)
C.