Error in running q2-fmt

I am trying to run q2-fmt to investigate the translocation of gut microbiome to certain tumors. I put the "intestine" samples as donors and "tumors" as the recipient and added the appropriate sample ids into the respective columns.

Metadata - transloc-tumor.tsv (2.2 KB)

I got an error that says 0.0 was not found as a group within the distribution. after running the below code

qiime fmt engraftment --i-diversity-measure core-metrics-transloc/faith_pd_vector.qza
--m-metadata-file transloc-tumor.tsv 
--p-compare baseline 
--p-time-column week 
--p-reference-column InitialDonorSampleID 
--p-subject-column SubjectID
--p-filter-missing-references
--p-against-group 0 
--p-p-val-approx asymptotic 
--o-stats stats.qza 
--o-raincloud-plot raincloud-plot.qzv

Could anyone help me identify what's wrong?

1 Like

Good evening.
I see, that --p-where '[SampleType]="stool"'
is absent.

Regards, sn

Thanks @5cr34m, I included the "where" line previously and was advised by one of the creators of q2-fmt not to include it.

Ok, @macrobiome, could you please rerun the command with --verbose flag and post output here.
Regards, sn

Here you go. Thanks!

Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/q2-fmt-alpha/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in engraftment
File "/home/ubuntu/miniconda3/envs/q2-fmt-alpha/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/ubuntu/miniconda3/envs/q2-fmt-alpha/lib/python3.8/site-packages/qiime2/sdk/action.py", line 475, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/ubuntu/miniconda3/envs/q2-fmt-alpha/lib/python3.8/site-packages/q2_fmt/_engraftment.py", line 41, in engraftment
stats = wilcoxon_srt(distribution=time_dist, compare=compare,
File "", line 2, in wilcoxon_srt
File "/home/ubuntu/miniconda3/envs/q2-fmt-alpha/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/ubuntu/miniconda3/envs/q2-fmt-alpha/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/home/ubuntu/miniconda3/envs/q2-fmt-alpha/lib/python3.8/site-packages/q2_stats/_stats.py", line 155, in wilcoxon_srt
for comp_a, comp_b in comparisons:
File "/home/ubuntu/miniconda3/envs/q2-fmt-alpha/lib/python3.8/site-packages/q2_stats/_stats.py", line 207, in _comp_baseline
baseline_group = _get_reference_from_column(group, baseline_group,
File "/home/ubuntu/miniconda3/envs/q2-fmt-alpha/lib/python3.8/site-packages/q2_stats/_stats.py", line 296, in _get_reference_from_column
raise ValueError("%r was not found as a group within the distribution."
ValueError: 0.0 was not found as a group within the distribution.

Plugin error from fmt:

0.0 was not found as a group within the distribution.

See above for debug info.

Thanks.
Check structure of your tsv-file.
I see


commas are not in place, i think.

I am sorry I don't understand which commas you're talking about. I thought there were no commas in TSV files.

Hello.
Sorry, tabs in tsv, commas in csv.
My fault.

But structure need to be checked.

Hi @macrobiome and @5cr34m,
I think the issue is that the numeric timepoint "week" starts at 1 but the against-group parameter is 0.

--p-against-group 0 

Therefore it can't find timepoint 0 in your data.
:turtle:

1 Like

Vielen Dank, Chloe!
But tsv must be checked also

Hi @5cr34m,
There is no issue with the TSV format. That metadata should work.

1 Like