process rad tags only processes some files and not others

[Gina Sideli]

Hello Julian or other Stacks users,

I am using Stacks 2.41. I have GBS data that has already been de-multiplexed by the genome center. It did not contain inline barcode sequences, but it did have a padded seq in front of cut cite added from a genome center that needed to be removed and then reads were trimmed to a common length with gbstrim (a perl script). 

I then ran the process rad tags script, but only some of the files were processed, while others gave error of "unable to located any input files to process".

I tried running this command with a smaller amount of files, and still the same results- only some files were able to be detected and processed. I read about changing the p command to -1, -2, but it doesn't make sense why some files were processed. Does anyone have insight into this?

process_radtags -p /Users/sideli_almond/fastq_test/trimmed -o /Users/sideli_almond/process_radtags_test -e ApeKI -r -c -q

File names:

1_trim.fastq

2_trim.fastq

300_trim.fastq

etc..

Thank you.

Regards,

Gina 

[Catchen, Julian]

Hi Gina,

If you pass a directory to the process_radtags program as input then
make sure you have no other files in the directory besides the FASTQ
files. If you don't want to do that, you can run the program on each
file individually using the -f flag. This is assuming you have
single-end data.

julian

Gina Sideli wrote on 12/4/19 6:00 PM: