Minpath error qiime2picrust2

[Nabil Quraishi]

Hi,

I have used the qiime2 picrust2 plugin for metagenome predictions and its worked well. I am now trying to run minpath using the ko_metagenome.qza that was generated. I have converted it to a tsv file with the first column as #OTUID (denotes KOs) and the subsequent columns are samples. I have a KO mapping file. When I run run_minpath.py I get this error: Error: required column "function" not found in input metagenome table

Changing the first column ID to function results in a different error KeyError: "['Sample1'] not in index"

How do I resolve this please?

Thanks,

[Gavin Douglas]

Hi there,

Could you post the exact command you're running and the head of the files that that you're inputting?

Thanks,

Gavin

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[Nabil Quraishi]

Thanks for your reply.

Command:

run_minpath.py -i q2-picrust2_output/ko_metagenome/ko.txt \

-o q2-picrust2_output/ko_metagenometsv/pathways_out \

--intermediate picrust/q2-picrust2_output/ko_metagenometsv/minpath_working \

-m picrust/q2-picrust2_output/keggpathwaymap.txt \

-p 10

Attached the head of the input file - this was generated by converting the ko_metagenome.qza generated by the pipeline to a tsv file through QIIME export.

I have even tried changing the heading to combinations of function, sequence, sampleid, but this didnt work.

Thanks,

Nabil

[Nabil Quraishi]

Hi,

Minpath gives the same error with the test data pred_metagenome_unstrat.tsv in the Picrust folder. If i rename the first column as function, I still get this error - KeyError: "[]" not in index

Would be grateful if there are any solutions or work arounds. Thanks

[Gavin Douglas]

Hi there,

What version are you using and do all the tests pass (warnings are ok) if you run “pytest” in the main picrust2 folder?

Gavin

[Nabil Quraishi]

I'm using the current version of Picrust - reinstalled it again. Pytest works perfectly fine with no warnings. I even tried to run using the main picrust pipeline  (rather than the qiime2 plugin, epa-ng and gapps installed with files in placement folder). It just gives the same Keyerror. Could I send you part of my datafile please to see if you are able to get it to work?

[Gavin Douglas]

Sure feel free to send it to me privately. Please send me the mapping file you’re using as well since that may be related to this error.

Best,

Gavin

[Gavin Douglas]

Thanks for sending me your file. You need to add the option “—no_regroup” to not use the default regrouping file, which was causing your table to be empty. This was impossible to figure out from the reported error alone though so I will be sure to make this clearer in the next release. Sorry for the inconvenience.

Best,

Gavin

[Nabil Quraishi]

Thanks Gavin, that error no longer appears but instead I get a new one:

 File "/home/ubuntu/drive/downloads/picrust2/picrust2/run_minpath.py", line 827, in pathway_abun_and_coverage

    pathway_abun = sum(subset_reaction_abun) / len(subset_reaction_abun)

ZeroDivisionError: division by zero

:(

[Nabil Quraishi]

Don't worry, fixed it. It was a problem with the mapping file - won't take spaces! Massive thanks for your help Gavin.

[Gavin Douglas]

Good to hear, no problem!