Picrust2 errors & fixes

[roylejw]

Hey Khi Pin,

Just a few notes for PICrust2:

1. When running it while skipping Naive-Bayse classification, Nextflow fails due to the workflow trying to call on 'export_biom.out.biom_vsearch', which is the default biom when NB is run. To fix this, I changed 'export_biom.out.biom_vsearch' to 'export_biom_skip_nb.out.biom_vsearch' in the workflow.
2. Same issue with AWS as before - by default it tries to run on minimal RAM and crashes AWS Batch. To fix this, I've hardcoded in the same fix for the other parts to get it running on AWS:

• cpus params.vsearch_cpu
• memory '150GB'

Those fixes have it running smoothly on AWS for me.

Cheers, Jack

[proteinosome]

Thanks @roylejw . Will file this under enhancement. The picrust2 part is definitely an oversight as I don't test skip_nb with picrust. Thanks for catching that.

[LuyangSong]

Hey Khi Pin, I encountered this problem and I don’t know how to solve it.

Command error:
  Traceback (most recent call last):
    File "/public/home/wyzhang/nf_conda/qiime2-2023.2-py38-linux-conda-2896a93e7b59af2808e11288fdd44ff0/bin/qiime", line 7, in <module>
      from q2cli.__main__ import qiime
    File "/public/home/wyzhang/nf_conda/qiime2-2023.2-py38-linux-conda-2896a93e7b59af2808e11288fdd44ff0/lib/python3.8/site-packages/q2cli/__main__.py", line 11, in <module>
      import q2cli.commands
    File "/public/home/wyzhang/nf_conda/qiime2-2023.2-py38-linux-conda-2896a93e7b59af2808e11288fdd44ff0/lib/python3.8/site-packages/q2cli/commands.py", line 11, in <module>
      import q2cli.builtin.dev
    File "/public/home/wyzhang/nf_conda/qiime2-2023.2-py38-linux-conda-2896a93e7b59af2808e11288fdd44ff0/lib/python3.8/site-packages/q2cli/builtin/dev.py", line 11, in <module>
      from q2cli.click.command import ToolCommand, ToolGroupCommand
    File "/public/home/wyzhang/nf_conda/qiime2-2023.2-py38-linux-conda-2896a93e7b59af2808e11288fdd44ff0/lib/python3.8/site-packages/q2cli/click/command.py", line 19, in <module>
      import click.core
  ModuleNotFoundError: No module named 'click.core'

Work dir:
  /public/home/wyzhang/pb-16S-nf/work/c4/0342bf1ddfe793d4cc988138dcb8fa

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

Please give me some suggestions, thank you very much！

[proteinosome]

Hi @LuyangSong please open a separate ticket for this issue and share .nextflow.log for troubleshooting. Thank you.