Debug help with core-metrics

Hi qiime people,

Chloe is out of town and I am confused on this error. Please help! Not sure why it is failing.

  • module load qiime2/2023.7

  • '[' -z '' ']'

  • case "$-" in

  • __lmod_sh_dbg=x

  • '[' -n x ']'

  • set +x
    Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
    Shell debugging restarted

  • unset __lmod_sh_dbg

  • return 0

  • qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table class_collapsed-table7.qza --p-sampling-depth 10000 --m-metadata-file Bf_metadata.tsv --output-dir class_core-metrics-collapsed-results
    Plugin error from diversity:

    Command '['faithpd', '-i', '/tmp/kac765/3959406/qiime2/kac765/data/cf86cd9d-9c2c-40b4-a004-1ca6e4210e52/data/feature-table.biom', '-t', '/tmp/kac765/3959406/qiime2/kac765/data/f2518f27-3b16-4a50-9e69-1c105b4b4e6f/data/tree.nwk', '-o', '/tmp/kac765/3959406/q2-AlphaDiversityFormat-zrtgjw2r']' returned non-zero exit status 1.

1 Like

Hey @kac765!

Can you re-run your command with the --verbose flag and then share that output in your response? This will give us a more detailed traceback to better identify where the error is coming from. Thanks! :lizard:


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