qiime/qiime — pull request #771 by gregcaporaso (2013-03-18 21:00:31+00:00)
Title: reverting #659 - this isn't actually working for me

here's some output where I added ``print file_names`` between lines 90 and 91 of ``scripts/collate_alpha.py``, using test data from ``qiime_test_data``:

```
core_diversity_analyses.py -i $PWD/otu_table.biom -o $PWD/core_output -m $PWD/map.txt -c SampleType,day -t $PWD/rep_set.tre -e 20 -v --suppress_beta_diversity --suppress_taxa_summary
Generate BIOM table summary
print_biom_table_summary.py -i /Users/caporaso/outbox/core_diversity_analyses/otu_table.biom -o /Users/caporaso/outbox/core_diversity_analyses/core_output/biom_table_summary.txt --suppress_md5
Filter low sequence count samples from table (minimum sequence count: 20)
filter_samples_from_otu_table.py -i /Users/caporaso/outbox/core_diversity_analyses/otu_table.biom -o /Users/caporaso/outbox/core_diversity_analyses/core_output/table_mc20.biom -n 20
Alpha rarefaction
python /Users/caporaso/code/Qiime/scripts/multiple_rarefactions.py -i /Users/caporaso/outbox/core_diversity_analyses/core_output/table_mc20.biom -m 10 -x 20 -s 1 -o /Users/caporaso/outbox/core_diversity_analyses/core_output/arare_max20//rarefaction/
Alpha diversity on rarefied OTU tables
python /Users/caporaso/code/Qiime/scripts/alpha_diversity.py -i /Users/caporaso/outbox/core_diversity_analyses/core_output/arare_max20//rarefaction/ -o /Users/caporaso/outbox/core_diversity_analyses/core_output/arare_max20//alpha_div/ -t /Users/caporaso/outbox/core_diversity_analyses/rep_set.tre
Collate alpha
python /Users/caporaso/code/Qiime/scripts/collate_alpha.py -i /Users/caporaso/outbox/core_diversity_analyses/core_output/arare_max20//alpha_div/ -o /Users/caporaso/outbox/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/
Traceback (most recent call last):
File "/Users/caporaso/.virtualenvs/qiime/bin/core_diversity_analyses.py", line 176, in
main()
File "/Users/caporaso/.virtualenvs/qiime/bin/core_diversity_analyses.py", line 173, in main
status_update_callback=status_update_callback)
File "/Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime/workflow/core_diversity_analyses.py", line 264, in run_core_diversity_analyses
status_update_callback=status_update_callback)
File "/Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime/workflow/downstream.py", line 420, in run_alpha_rarefaction
close_logger_on_success=close_logger_on_success)
File "/Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime/workflow/util.py", line 117, in call_commands_serially
raise WorkflowError, msg
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Collate alpha
Command run was:
python /Users/caporaso/code/Qiime/scripts/collate_alpha.py -i /Users/caporaso/outbox/core_diversity_analyses/core_output/arare_max20//alpha_div/ -o /Users/caporaso/outbox/core_diversity_analyses/core_output/arare_max20//alpha_div_collated/
Command returned exit status: 1
Stdout:
['alpha_rarefaction_10_0.biom', 'alpha_rarefaction_10_1.biom', 'alpha_rarefaction_10_2.biom', 'alpha_rarefaction_10_3.biom', 'alpha_rarefaction_10_4.biom', 'alpha_rarefaction_10_5.biom', 'alpha_rarefaction_10_6.biom', 'alpha_rarefaction_10_7.biom', 'alpha_rarefaction_10_8.biom', 'alpha_rarefaction_10_9.biom', 'alpha_rarefaction_11_0.biom', 'alpha_rarefaction_11_1.biom', 'alpha_rarefaction_11_2.biom', 'alpha_rarefaction_11_3.biom', 'alpha_rarefaction_11_4.biom', 'alpha_rarefaction_11_5.biom', 'alpha_rarefaction_11_6.biom', 'alpha_rarefaction_11_7.biom', 'alpha_rarefaction_11_8.biom', 'alpha_rarefaction_11_9.biom', 'alpha_rarefaction_12_0.biom', 'alpha_rarefaction_12_1.biom', 'alpha_rarefaction_12_2.biom', 'alpha_rarefaction_12_3.biom', 'alpha_rarefaction_12_4.biom', 'alpha_rarefaction_12_5.biom', 'alpha_rarefaction_12_6.biom', 'alpha_rarefaction_12_7.biom', 'alpha_rarefaction_12_8.biom', 'alpha_rarefaction_12_9.biom', 'alpha_rarefaction_13_0.biom', 'alpha_rarefaction_13_1.biom', 'alpha_rarefaction_13_2.biom', 'alpha_rarefaction_13_3.biom', 'alpha_rarefaction_13_4.biom', 'alpha_rarefaction_13_5.biom', 'alpha_rarefaction_13_6.biom', 'alpha_rarefaction_13_7.biom', 'alpha_rarefaction_13_8.biom', 'alpha_rarefaction_13_9.biom', 'alpha_rarefaction_14_0.biom', 'alpha_rarefaction_14_1.biom', 'alpha_rarefaction_14_2.biom', 'alpha_rarefaction_14_3.biom', 'alpha_rarefaction_14_4.biom', 'alpha_rarefaction_14_5.biom', 'alpha_rarefaction_14_6.biom', 'alpha_rarefaction_14_7.biom', 'alpha_rarefaction_14_8.biom', 'alpha_rarefaction_14_9.biom', 'alpha_rarefaction_15_0.biom', 'alpha_rarefaction_15_1.biom', 'alpha_rarefaction_15_2.biom', 'alpha_rarefaction_15_3.biom', 'alpha_rarefaction_15_4.biom', 'alpha_rarefaction_15_5.biom', 'alpha_rarefaction_15_6.biom', 'alpha_rarefaction_15_7.biom', 'alpha_rarefaction_15_8.biom', 'alpha_rarefaction_15_9.biom', 'alpha_rarefaction_16_0.biom', 'alpha_rarefaction_16_1.biom', 'alpha_rarefaction_16_2.biom', 'alpha_rarefaction_16_3.biom', 'alpha_rarefaction_16_4.biom', 'alpha_rarefaction_16_5.biom', 'alpha_rarefaction_16_6.biom', 'alpha_rarefaction_16_7.biom', 'alpha_rarefaction_16_8.biom', 'alpha_rarefaction_16_9.biom', 'alpha_rarefaction_17_0.biom', 'alpha_rarefaction_17_1.biom', 'alpha_rarefaction_17_2.biom', 'alpha_rarefaction_17_3.biom', 'alpha_rarefaction_17_4.biom', 'alpha_rarefaction_17_5.biom', 'alpha_rarefaction_17_6.biom', 'alpha_rarefaction_17_7.biom', 'alpha_rarefaction_17_8.biom', 'alpha_rarefaction_17_9.biom', 'alpha_rarefaction_18_0.biom', 'alpha_rarefaction_18_1.biom', 'alpha_rarefaction_18_2.biom', 'alpha_rarefaction_18_3.biom', 'alpha_rarefaction_18_4.biom', 'alpha_rarefaction_18_5.biom', 'alpha_rarefaction_18_6.biom', 'alpha_rarefaction_18_7.biom', 'alpha_rarefaction_18_8.biom', 'alpha_rarefaction_18_9.biom', 'alpha_rarefaction_19_0.biom', 'alpha_rarefaction_19_1.biom', 'alpha_rarefaction_19_2.biom', 'alpha_rarefaction_19_3.biom', 'alpha_rarefaction_19_4.biom', 'alpha_rarefaction_19_5.biom', 'alpha_rarefaction_19_6.biom', 'alpha_rarefaction_19_7.biom', 'alpha_rarefaction_19_8.biom', 'alpha_rarefaction_19_9.biom', 'alpha_rarefaction_20_0.biom', 'alpha_rarefaction_20_1.biom', 'alpha_rarefaction_20_2.biom', 'alpha_rarefaction_20_3.biom', 'alpha_rarefaction_20_4.biom', 'alpha_rarefaction_20_5.biom', 'alpha_rarefaction_20_6.biom', 'alpha_rarefaction_20_7.biom', 'alpha_rarefaction_20_8.biom', 'alpha_rarefaction_20_9.biom']

Stderr
Traceback (most recent call last):
File "/Users/caporaso/code/Qiime/scripts/collate_alpha.py", line 126, in
main()
File "/Users/caporaso/code/Qiime/scripts/collate_alpha.py", line 99, in main
example_fname = file_names[file_name_table.index(sorted_fname_table[0])]
IndexError: list index out of range
```