mothur

Otu.association doesn't work with metadata new versions


#1

otu.association doesn’t work with metadata in v1.41.1 (or v1.41.0 or v1.40.5).
However, it works fine in v1.36.1
otu.association works fine in all versions without metadata

Is it possible to fix this in the new versions?
Thanks,


#2

Can you post the exact syntax of the command you are running and what the error message is?


#3

Hi Pat,

I’ve attached a link to PDF with the screenshots that show the version, the command, the files I have used and the crash that occurs in v1.41.1 compared to things working well in v1.36.1.

Please let me know if you need any further clarification. When I noticed this problem with v1.41.1 I tested older versions (v1.41.0 and v1.40.5) and they have an identical problem, that I haven’t screenshotted today.

I used the same command in all versions:

otu.association(shared=file.shared, metadata=file.metadata)

And I used the same files each time, in a new folder where the relevant mothur version is.

The otu.association command itself works fine without metadata in v1.41.1 (screenshot attached)

otu.association(shared=file.shared)

Also, with:

otu.association(shared=file.shared, metadata=file.metadata)

If there is a spelling mistake typed in the metadata file, when using v1.36.1 the expected error is returned and one can proceed as normal (screenshot attached, e.g. I purposely left the K out of Karijini in the filename). However, if there is a spelling mistake typed in the metadata file, when running this command using v1.41.1 the entire computer hangs (seriously, as in, can’t even press Ctrl+Alt+Del. This has happened multiple times, I have tested on two different computers, but obviously I can’t get a screenshot as the computer has to be forced to reboot).

Thanks for your help,

Emma

https://drive.google.com/open?id=1Mrjh5Qf94Ke_K5IrSJMhZvh7WeEazPhL


#4

Thanks for reporting this bug. Mothur was failing to save the metadata associated with the groups. I have fixed the issue and the change will be part of our next release. In the meantime you can work around the issue by manually specifying the groups. For example:

mothur > otu.association(shared=stability.opti_mcc.shared, metadata=mouse.dpw.metadata) - will fail

but

mothur > otu.association(shared=stability.opti_mcc.shared, metadata=mouse.dpw.metadata, groups=F3D0-F3D1-F3D2-F3D3-F3D4-F3D5-F3D6-F3D7-F3D8-F3D9-F3D141-F3D142-F3D143-F3D144-F3D145-F3D146-F3D147-F3D148-F3D149-F3D150) - runs fine

Sorry for the inconvenience, and thanks again for helping us to maintain mothur.


#5

Thanks Sarah and Pat,

Really appreciate it!


#6

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