ekopylova/qiime — pull request #1 by josenavas (2014-07-10 17:21:03+00:00)
Title: Tests for new open ref workflow

@ekopylova This PR against your new-software-otu-picking branch adds the tests to the new open reference pipeline. However, the pipelines is failing, and I'm not familiar enough with the code to fix it. Here is the error:

```
python tests/test_workflow/test_pick_open_reference_otus.py PickSubsampledReferenceOtusThroughOtuTableTests.test_pick_subsample_open_reference_otus_sortmerna_sumaclust
E
======================================================================
ERROR: test_pick_subsample_open_reference_otus_sortmerna_sumaclust (__main__.PickSubsampledReferenceOtusThroughOtuTableTests)
pick_subsampled_open_reference_otus functions as expected with
----------------------------------------------------------------------
Traceback (most recent call last):
File "tests/test_workflow/test_pick_open_reference_otus.py", line 494, in test_pick_subsample_open_reference_otus_sortmerna_sumaclust
status_update_callback=no_status_updates)
File "/Users/jose/qiime_software/qiime/qiime/workflow/pick_open_reference_otus.py", line 920, in pick_subsampled_open_reference_otus
close_logger_on_success=False)
File "/Users/jose/qiime_software/qiime/qiime/workflow/util.py", line 122, in call_commands_serially
raise WorkflowError(msg)
WorkflowError:

*** ERROR RAISED DURING STEP: Make the otu table
Command run was:
make_otu_table.py -i /tmp/qiime_wf_outYXJbtY/final_otu_map_mc2.txt -o /tmp/qiime_wf_outYXJbtY/otu_table_mc2.biom
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
File "/Users/jose/qiime_software/qiime/scripts/make_otu_table.py", line 99, in
main()
File "/Users/jose/qiime_software/qiime/scripts/make_otu_table.py", line 93, in main
otu_ids_to_exclude=ids_to_exclude)
File "/Users/jose/qiime_software/qiime/qiime/make_otu_table.py", line 84, in make_otu_table
create_date=datetime.now().isoformat())
File "/Users/jose/qiime_software/biom-format/biom/table.py", line 262, in __init__
self._verify_metadata()
File "/Users/jose/qiime_software/biom-format/biom/table.py", line 401, in _verify_metadata
raise TableException("Duplicate observation_ids")
biom.exception.TableException: Duplicate observation_ids

----------------------------------------------------------------------
Ran 1 test in 42.062s

FAILED (errors=1)
```