parameter file not working in pick_open_reference_otus.py / sortmerna_sumaclust

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jfg

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May 16, 2017, 11:31:22 AM5/16/17
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Howdy all,

   Searched for this problem on the forum but most similar issue was not the same- 


   I'm trying open-reference otu picking with sumaclust/sortmeRNA with the following call:
pick_open_reference_otus.py -i '/home/eri/jf/DW/dw_ac_splib/dw_ac_all_tags.seqOut' -o '/home/eri/jf/DW/dw_ac_smr_sumac'  -p '/home/eri/jf/q_params.txt' -m sortmerna_sumaclust


   - and have set the my parameters file as below:
pick_open_reference_otus:otu_picking_method sortmerna_sumaclust
pick_open_reference_otus:reference_fp /media/cart/cart_sandbox/db_Databases/silva128/97_rep_set_otus_all.fasta
pick_open_reference_otus
:parallel True
pick_open_reference_otus
:jobs_to_start 20
pick_open_reference_otus
:percent_subsample 0.01
pick_open_reference_otus
:min_otu_size 3



   However in the output logfiles, pick_otus.py steps flag -m uclust as the picking method. UCLUST is the default method, so I assume that for some reason the parameter file is not being applied properly (despite the fact it appears called at the top of the log), e.g.:
parameter file values:
[...]
pick_open_reference_otus.py:otu_picking_method sortmerna_sumaclust
[...]

# Pick Reference OTUs command
pick_otus
.py -i /home/eri/jf/DW/dw_ac_splib/dw_ac_all_tags.seqOut -o dw_ac_smr_sumac/step1_otus -r /home/eri/jf/MV_i/db_silva_128/rep_all_97_otus.fasta -m uclust_ref  --suppress_new_clusters



Any insight would be appreciated! Print_qiime_config output appended for the sheer joy of it.
jfg



dw_ac_log.txt
eri_qiime_test.txt
q_params.txt

Evan Bolyen

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May 16, 2017, 5:31:41 PM5/16/17
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Hi!

It looks like the problem is your parameters file is using the workflow name (pick_open_reference_otus) instead of the steps that that workflow runs (pick_otus).

For example, the first line is currently:
pick_open_reference_otus:otu_picking_method sortmerna_sumaclust

However, it should be:
pick_otus:otu_picking_method sortmerna_sumaclust

As a heads up, it also looks like the rest of your parameters are referencing the parameter names of the workflow instead of the underlying script. So they will all need to be removed and passed directly into your pick_open_reference.py command. (Basically you should just need one line in your parameters file.)
Here is some further documentation about formatting the parameter files.

Hope that helps!
-Evan

jfg

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May 17, 2017, 8:25:11 AM5/17/17
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Brilliant Evan, that makes a lot of sense. And thanks for the pointer on renaming parameters to be in line with the script being called - that could well have cost me a coffee break. 

-jfg
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