Hi all,
I'm trying to run the script for the open_otu_picking with QIIME but there is some error to assign the taxonomy so I used the --suppress_taxonomy_assignment option. That means I have to generate another OTU table and the taxonomy for myself using the outputs from the last step in the alignment. I'm not sure about which input I have to use as if I use the final_otu_map_mc2.txt generated at the end of the step 4, that means I have to align the samples for my own and to omit then the failures from the alignment. Which is ok, but I'm wondering if there is other way to do it.
(I've used Silva_119_rep_set_97.fna as -r )
Thanks in advanced.
Hi Beatriz,
Is the error that you are getting related to the gap (-) symbol? If the database that you are using has aligned 16S rRNA gene sequences, so your sample sequences need to be aligned as well. Otherwise you might need to use the greengenes database if your sequences are not aligned. So use the pick_open_reference_otus.py command with the 97_otus.fasta database (should be pre-loaded on qiime, just search for it and copy into your directory, otherwise you can download it on the qiime page:
http://qiime.org/home_static/dataFiles.html
and select either 13_5 or 13_8)
Hope this helps!
Hi Riegardt,
Thanks for your comments.
Actually that is not the problem I'm getting running the pick_open_reference_otus.py. What happens is that I have to suppress the alignment and taxonomy assign as I cannot find the way to include the taxa file from SILVA for that stage (taxonomy_97_all_levels.txt). So I have to do the alignment and the taxonomy assignment apart from this script, but using the generated files: rep_seqs.fna. It is not that bad to do it separately but it is much easier to run just the pick_open_reference_otus.py command and get alignment, tree, taxonomy and .biom table just from one run.
As you mentioned, I used the pick_open_reference_otus.py command with the 97_otus.fasta, from SILVA_119.
The error that appearse is related with the id of the taxonomy_fp field which is necessary in the taxonomy step.
Regards!
I think you can run the taxonomy and reference seq files for assign_taxonomy through the pick_open_reference_otus.py by adding a parameter file e.g.
$ pick_open_reference_otus.py -p parameter_file.txt *rest of your command*
Attached is a parameter file that should work with your command you just need to modify the paths for the respective files and run the command again with the parameter file.
Hi Joseph,
Thanks, I think it would be the solution since I did no generate any parameter_file for the assign_taxonomy through the pick_open_reference_otus.py
Regards,
Bea.
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