alpha_rarefaction.py - fails when tree is not provided for non-phylogenetic metrics

[gregcaporaso]

When using alpha_rarefaction.py with the observed_species metric (which is non-phylogenetic), the workflow failed at the alpha_diversity.py step because the alpha_diversity.py commands contain '-t None', which causes the script to fail saying that it can't find the file 'None'.

These commands were found inside the file alpha_div/ALDIV_WMO_jobs.txt since I was running them in parallel. For example, here's one of the commands in the ALDIV_WMO_jobs.txt file:

{{{ /bin/bash ; /home/ubuntu/qiime_software/python-2.7.1-release/bin/python /home/ubuntu/qiime_software/qiime-1.5.0-release/bin/alpha_diversity.py -i /home/ubuntu/data/hiseq_its_113011/slout_7_1/arare_99_similarity_max_3147/rarefaction/rarefaction_323_6.biom -o /home/ubuntu/data/hiseq_its_113011/slout_7_1/arare_99_similarity_max_3147/alpha_div//ALDIVWMO/alpha_rarefaction_323_6.biom -t None -m observed_species }}}

I verified that this is a problem by running 'alpha_diversity.py -t None' and the script raises an error saying that the file 'None' can't be found. Thus, it seems that alpha_rarefaction.py is generating these commands incorrectly and shouldn't pass -t at all if there isn't a tree file to begin with.

I was using QIIME 1.5.0 on a 4-node cluster on EC2 (ami-e4bf1b8d) with 21 jobs to start. Here's the original command that I gave to qsub:

{{{ alpha_rarefaction.py -i /home/ubuntu/data/hiseq_its_113011/slout_7_1/otus_99_similarity/uclust_ref_picked_otus/otu_table.biom -o /home/ubuntu/data/hiseq_its_113011/slout_7_1/arare_99_similarity_max_3147 -m /home/ubuntu/data/hiseq_its_113011/map.txt -p /home/ubuntu/data/hiseq_its_113011/qiime_parameters_99_similarity.txt -aO 21 -e 3147 }}}

Here's my QIIME parameters file:

{{{

OTU picker parameters

pick_otus:enable_rev_strand_match True pick_otus:similarity 0.99

Alpha diversity parameters

alpha_diversity:metrics observed_species

Beta diversity parameters

beta_diversity:metrics bray_curtis }}}

[gregcaporaso]

Imported from trac issue 203. Created by jrideout on 2012-06-22T10:14:27, last modified: 2012-06-22T10:14:27

[gregcaporaso]

This has been fixed (line 952 of Qiime/qiime/workflow.py).