Question: Pindel configuration file seems not working
gravatar for cmonat
2.1 years ago by
cmonat0 wrote:

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!


ADD COMMENTlink written 2.1 years ago by cmonat0

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

ADD REPLYlink written 2.1 years ago by Rohit1.3k

Thank you for the idea but it doesn't work either, I have the same error message. Any other idea?



PS: I have also tried with path into the configuration file and it doesn't work either... :(

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by cmonat0

Did you use a tab or a space in the config file? Usually its a space, looks like you are using a tab

ADD REPLYlink written 2.1 years ago by Rohit1.3k

Ah yes, it was that! Thank you very much!

Have a nice day :)


ADD REPLYlink written 2.1 years ago by cmonat0
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