Error in running q2-fmt

[macrobiome (T)]

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?

[5cr34m (Nikonov_Sergey)]

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

Regards, sn

[macrobiome (T)]

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

Am I interpreting weighted vs. unweighted distance matrix unifrac boxplots correctly?

Hi @macrobiome, Good! I always have to check I misunderstood how your metadata was set up. There is no issue with your donor metadata column. However you will want to add a "fake" time column. I would put a column that is called week in your metadata. Give all the tumor values 1 and leave all the intestines blank. (This is part of the tweaking this method to fix your study) Lastly remove the filtering parameter, you will need all your samples in order to run this anaysis. --…

[5cr34m (Nikonov_Sergey)]

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

[macrobiome (T)]

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.

[5cr34m (Nikonov_Sergey)]

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

commas are not in place, i think.

[macrobiome (T)]

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

[5cr34m (Nikonov_Sergey)]

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

[5cr34m (Nikonov_Sergey)]

But structure need to be checked.

[cherman2 (Chloe Herman)]

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.

[5cr34m (Nikonov_Sergey)]

Vielen Dank, Chloe!
But tsv must be checked also

[cherman2 (Chloe Herman)]

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