split_libraries with run_prefix is returning zero sequences

Skip to first unread message

Jacob Cram

Jul 28, 2017, 5:40:00 PM7/28/17
to Qiime 1 Forum
Hello all,
     I have two plates worth of 454 fasta reads that I concatenated together, that I was hoping to demultiplex with split_libraries.py.
Split libraries works fine if I just apply it to one of the two plates. For a working example, one can run the following, with the attached files.

split_libraries.py -m mapping_file_test_prefix_plate1only.csv -f test_454_plate1only.fna -b 6 -z truncate_remove -o test_prefix_out_plate1only_norunprefix

In this case two of the five sequences (that I include in this toy example) make it through all of the filtering steps. So far, so good.

Now I combine the two fasta files and try to use the run_prefix example.

split_libraries.py -m mapping_file_test_prefix.csv -f test_454.fna -b 6 -z truncate_remove -o test_prefix_out -j run_prefix

In this case, none of the nine sequences in the merged fasta file make it into the output file. It seems like I must be misspelling the prefixes or something but I can't seem to find my mistake. Any advice?

Jose Antonio Navas Molina

Aug 7, 2017, 11:52:06 AM8/7/17
to Qiime 1 Forum
Hi Jacob,

I'm unsure on what is the source of the problem that you're facing. However, you don't need to combine the 2 fasta files in a single file to run through split_libraries.py. See the "Multiple FASTA and QUAL Files example" in the script documentation. The "-q" parameter is optional, so you can leave it out if you don't have the qual files and it should work as expected.

Hope this helps!

Jacob Cram

Aug 8, 2017, 8:41:48 PM8/8/17
to Qiime 1 Forum
That workaround seems to work. Thanks.
Reply all
Reply to author
0 new messages