SEPP fragment insertion plugin error

User Support
1

Hi all, I’m stuck with an error message I got after installing the qiime2 plugin q2_fragment_insertion (https://github.com/sjanssen2/q2-fragment-insertion)
When I try to run the following command:

qiime fragment-insertion sepp
–i-representative-sequences rep-seqs.qza
–o-tree insertion-tree.qza
–o-placements insertion-placements.qza

I get the following error:

Plugin error from fragment-insertion:
‘NoneType’ object has no attribute ‘rfind’
Debug info has been saved to /tmp/qiime2-q2cli-err-h6h8ywxc.log

Any ideas on what my issue is?

2

Hi @cmarotz,
Could you please post the full error message? Either:

  1. copy it from this file: /tmp/qiime2-q2cli-err-h6h8ywxc.log
  2. Or if that file no longer exists, you can re-run the command with --verbose added to the end of that command.

Then we can take a look. cc: @Stefan

Thanks!

3

Thanks Nicholas!
When I try and view the full error log it says file does not exist. I tried a few different techniques to expand this error log (adding --verbose as recommended, downloading and running locally instead of on a server, adding -e in my qsub command), but I can’t get any further information besides this 2 line output:

Plugin error from fragment-insertion:
‘NoneType’ object has no attribute ‘rfind’

Is there another way to get more debug info that I’m missing?

4

Hi Lisa,

could you please double check the version of the q2-fragment-insertion plugin in your environment, by copy & pasting the result of the command: conda list | grep frag

If you don’t mind, you could point me to your inputs on barnacle and I have a look from there.

Best,
Stefan

5

Hi Stefan,
Bingo! It turns out I had downloaded an older forked version, I updated to the current version and now it is running great:)

Thanks!
Lisa

6

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