Hi there,
I'm using Pindel, my configuration file looks like this:
But when I run Pindel I get the following message:
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
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
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
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)
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