Could you send me the version of the software and database? They should
both be v1.2.

On Nov 4, 2016 3:45 AM, "mherold1" [email protected] wrote:

Hello,

similarly to #20 #20 running
test_midas.py fails at this step:

./test_midas.py

....F.....

FAIL: test_help_text (main.MergeGenes)

Traceback (most recent call last):
File "./test_midas.py", line 132, in test_help_text
self.assertTrue(sum(self.retcodes)==0, msg=error)
AssertionError:

Failed to execute the command: merge_midas.py genes

---

Ran 10 tests in 252.652s

FAILED (failures=1)

I am running MIDAS on python 2.7.3

I traced back the error a bit and it probably comes from this call merge_midas.py
genes ./genes -i ./sample -t list --species_id Bacteroides_vulgatus_57955
--sample_depth 0.0, when I run it separately it shows the following error
message:

[...]
Identifying species
found 1 species with sufficient high-coverage samples

Merging: Bacteroides_vulgatus_57955 for 1 samples
Traceback (most recent call last):
File "/work/local_tools/MIDAS/scripts/merge_midas.py", line 352, in
run_program(program, args)
File "/work/local_tools/MIDAS/scripts/merge_midas.py", line 339, in run_program
merge_genes.run_pipeline(args)
File "/work/local_tools/MIDAS/midas/merge/merge_genes.py", line 109, in run_pipeline
read_cluster_map(sp, args['db'], args['cluster_pid'])
File "/work/local_tools/MIDAS/midas/merge/merge_genes.py", line 97, in read_cluster_map
sp.map[r['centroid_99']] = r['centroid_%s' % pid]
KeyError: 'centroid_95'

Do you know why this happens?

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from midas.

I was using db 1.1, I will retry after updating

from midas.

Updating to v1.2 fixed the problem

from midas.