Hello I am using the demultiplex/variant caller pipeline for GBS called GBS-POD \https://github.com/carolyncaron/GBSpipeline/wiki/GBS-pipeline-POD
I keep running into this error: greg@Genomics:/media/greg/Overflow/gbs3/GBSpipeline$ ./GBS_pipeline.pl demultiplex Adzuki_ExB_Plate1 indextopsbottoms.txt TGCA readsR1plate1.fastq readsR2plate1.fastq processedreads given is experimental at ./GBS_pipeline.pl line 114. when is experimental at ./GBS_pipeline.pl line 117. when is experimental at ./GBS_pipeline.pl line 161. when is experimental at ./GBS_pipeline.pl line 196. when is experimental at ./GBS_pipeline.pl line 232. Calling demultiplex ... ERROR: Unexpected number of columns in indextopsbottoms.txt: 97
As far as I know I have a tab delimited text file .txt, which only has 2 columns (name, sequence) and 96 rows which are the 96 index sequences.
This is the script: open (INDICES, $index_file) or die "ERROR: Unable to open $index_file.\n"; my $first_line = <indices>; chomp $first_line; $first_line =~ s/ //g; my @columns = split(/\t/, $first_line); my $num_col = ($#columns)+1; if ($num_col > 2) { die "ERROR: Unexpected number of columns in $index_file: $num_col \n"; } # Since we already looked at the first line, add its contents to the array of indices and samples hash, # then iterate over the remainder of the file elsif ($num_col == 2)
