Process_radtags error: "too many columns specified in BC8.txt"

[hcha...@ucdavis.edu]

Hello,

I am new to stacks and having issues with process_radtags. I am working with DNA that was digested with one restriction enzyme, but has two combinatorial inline barcodes per sample. I used the following code:

process_radtags -i gzfastq -P -1 \

/lustre1/hch84976/workDir/hchGbsOutput/rawL1/HNLFTBGX3_L1_R1.fastq.gz -2 \

/lustre1/hch84976/workDir/hchGbsOutput/rawL1/HNLFTBGX3_L1_R2.fastq.gz \

-b BC8.unix.txt -o /lustre1/hch84976/workDir/hchGbsOutput/L1_processed -c -q -r \

--inline_inline -e apeKI --adapter_mm 1 1>job.out 2>job.err

But I get the error: "Too many columns (5) specified in 'BC8.unix.txt' on line 1"

Does anybody know why this issue is arising? My barcode file is a text file with the format 'BARCODE1<tab>BARCODE2<tab>SAMPLENAME', which is the format specified in the manual. Any suggestions are greatly appreciated! 

Thanks!

[Nicolas Rochette]

Hi hcha...@ucdavis.edu

> My barcode file is a text file with the format
> 'BARCODE1<tab>BARCODE2<tab>SAMPLENAME',

Apparently not, as the error is that there are five columns.

You want to check the output of the command:

od -a BC8.unix.txt

Best,

Nicolas

[hcha...@ucdavis.edu]

Thanks Nicolas. The problem was that I converted an Excel file to tab delimited text, resulting in two empty columns being imported. 

~Hannah