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Code, unit tests, and tutorials for running PICRUSt2
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Open file error picrust2_out_pipeline/intermediate/pathways/minpath_running/Unnamed: #239

Closed bobems1215 closed 2 years ago

bobems1215 commented 2 years ago

Hello,

I did see this issue raised in a closed thread but I wanted to bring it back up because I don't think a solution was ever found. For some reason, a file named "Unnamed: 21_minpath_in.txt" is being made during the pathway_pipeline.py command.

I tried looking in the scripts but I can not see where this file would be created. I also don't know if this file is something that the picrust scripts are making or if this is being created from Minpath itself.

Any guidance on this issue would be appreciated.

Thanks!

Bob

gavinmdouglas commented 2 years ago

Hey @bobems1215,

Can you confirm that every column in your input table has a sample name? Perhaps an integer sample name could be causing this problem as well.

Cheers,

Gavin

bobems1215 commented 2 years ago

Hey Gavin,

Yep, every column in my input table has a sample name. Attached is a screenshot of the head of my count table.

Head_Of_Input_table

My next step is to try and convert this to .biom format (right now it is just a count table in txt form).

Thanks again,

Bob

gavinmdouglas commented 2 years ago

Hi Bob, did you ever resolve this problem? I would be happy to try to reproduce the problem if you don't mind sharing your infiles. You could email them to me if so:

gmail_screenshot
gavinmdouglas commented 2 years ago

Hey again,

I was able to produce this problem when inputting certain malformed sequence abundance tables. I have added some sanity checks in the latest version (v2.5.0) which should help determine what the problem is with your input table. It is very likely an issue of a malformed table (e.g., an extra column on one line) in your case.

Cheers,

Gavin

bobems1215 commented 2 years ago

Hey Gavin,

Sorry for the late reply. Yeah, I was able to actually run this by transforming my sequence abundance table from a .tsv to a .biome file. So I think you are right that there was some extra column in there that got removed in the transfer. It was easy enough to transform into a biome file that we stuck with it throughout but I will go back in and try the updated version to see if my original files will work.

Thanks!

Bob

On Thu, Apr 28, 2022 at 3:06 PM Gavin Douglas @.***> wrote:

Hey again,

I was able to produce this problem when inputting certain malformed sequence abundance tables. I have added some sanity checks in the latest version (v2.5.0) which should help determine what the problem is with your input table. It is very likely an issue of a malformed table (e.g., an extra column on one line) in your case.

Cheers,

Gavin

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gavinmdouglas commented 2 years ago

Good to hear!