Getting representative sequences

Skip to first unread message

Jeyamalar Jeyanathan

May 26, 2020, 8:40:57 AM5/26/20
to Qiime 1 Forum
I want to have the representative sequences (fasta) belong to one genus. Can anyone help me how I can get this in Qiime 1. The out picking method I used was open reference. 

Thank you

Jeyamalar Jeyanathan

May 26, 2020, 8:44:03 AM5/26/20
to Qiime 1 Forum
I want to have all the representative sequences of the genus Prevotella. I used Qiime 1 and open reference OTU picking.


May 26, 2020, 9:37:03 AM5/26/20
to Qiime 1 Forum

There should be an taxonomic assignments file, that matches the representative sequence identifier to the taxonomy strings. (I think it will be in the uclust_assigned_taxonomy).

If you can find this file, maybe you can do a grep command like this:
grep "Prevotella" X > prevotella_ids.txt
where X is the taxonomic assignments file.

Then the desired IDs should be in the prevotella_ids.txt file.

Next filter the rep_set.fna file with the script and pass the prevotella_ids.txt file as the --seq_id_fp parameter.


Aug 19, 2020, 3:35:28 PM8/19/20
to Qiime 1 Forum
Dear Tony,
Thank you. I got all the sequences.

Best regards,


Nov 24, 2020, 11:06:21 AM11/24/20
to Qiime 1 Forum
Hello sir
Hope you are fine and doing good.
Please have a look at my error while running the command
As I am getting an unwanted error
Traceback (most recent call last):
  File "/usr/local/bin/", line 162, in <module>
  File "/usr/local/bin/", line 158, in main
    disable_primer_check, added_demultiplex_field, suppress_html)
  File "/usr/local/lib/python2.7/dist-packages/qiime/", line 97, in check_mapping_file
    added_demultiplex_field, strip_quotes=False, suppress_stripping=True)
  File "/usr/local/lib/python2.7/dist-packages/qiime/", line 182, in process_id_map
  File "/usr/local/lib/python2.7/dist-packages/qiime/", line 822, in check_header
    desc_ix, bc_ix, linker_primer_ix, added_demultiplex_field)
  File "/usr/local/lib/python2.7/dist-packages/qiime/", line 888, in check_header_required_fields
    if (header[curr_check] != header_checks[curr_check] and
IndexError: list index out of range
Please help me out

Reply all
Reply to author
0 new messages