.99997 process_radtags Unable to locate any input files

[brian simison]

I am playing with the 0.99997 process_radtags to process double-digested, paired-end, Illumina HiSeq data using combinatorial barcodes.

my command is:

process_radtags -P -p /Data/Rad_tag/raw -b /Data/Rad_tag/Docs/ddBarcode_index_stacks.txt -o ./proc_radtag_dd/ -c -q -r --index_index --renz_1 sphI --renz_2 mluCI -i gzfastq

I am using full paths here and I get:

Unable to locate any input files to process within '/Data/Rad_tag/raw/'

Found 0 paired input file(s).

Searching for single-end, inlined and paired-end, indexed barcodes.

Loaded 192 barcodes (5bp / 6bp).

Closing files, flushing buffers...

Outputing details to log: './proc_radtag_dd/process_radtags.log'

my input file name format is "Sample_CASRADs120912_ACAGTG.R1.fastq" I tried:

1) renaming input files to match file name convention on Stacks tutorial page for this kind of data.

2) I have tried '--index_index' and '--inline_index' with same results.

3) I have tried with '-i gzfastq' and '-i fastq' on both .gz and .fastq files.

4) I have confirmed that files are in the dir and that they are intact.

The result is the same error message.

Any ideas on what I am doing wrong?

[brian simison]

After trying various input file names, it turns out that the name must have underscores between text and must have a matching number after the R1 and R2 of the paired reads. So my file names changed to "Sample_CASRADs120912_ACAGTG_R1_001.fastq" and "Sample_CASRADs120912_ACAGTG_R2_001.fastq" work. The next pair must have "..._R1_002.fastq" and "..._R2_002.fastq" and so on.