split_libraries with run_prefix is returning zero sequences

18 views
Skip to first unread message

Jacob Cram

unread,
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?
mapping_file_test_prefix.csv
mapping_file_test_prefix_plate1only.csv
test_454.fna
test_454_plate1only.fna
qiime_config.txt

Jose Antonio Navas Molina

unread,
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

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