Error with 'sourmash tax genome' command

[agombolay]

I would like to run sourmash tax genome using the CSV file generated from fastgather rather than gather. However, when I run sourmash tax genome with the fastgather CSV, I receive the following error message:

sourmash tax genome --gather-csv sample.fastgather.csv --taxonomy-csv gtdb-rs214.lineages.csv.gz --output-dir sourmash_output
Error Message: ERROR: 'sample.fastgather.csv' is missing columns needed for taxonomic summarization.

[ctb]

hi @agombolay thanks for reporting!

could you please share the headers for your sample.fastgather.csv file (head -1 sample.fastgather.csv) as well as the output of sourmash info -v? thanks!

[agombolay]

Headers: query_filename,rank,query_name,query_md5,match_name,match_md5,intersect_bp

== This is sourmash version 4.8.8. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

sourmash version 4.8.8

• loaded from path: /path/.conda/envs/sourmash/lib/python3.12/site-packages/sourmash/cli

khmer version: None (internal Nodegraph)

screed version 1.1.3

• loaded from path: /path/.conda/envs/sourmash/lib/python3.12/site-packages/screed

the following plugins are installed:

plugin type from python module v entry point name

---

sourmash.cli_script sourmash_plugin_branchwater 0.9.3 manysearch
sourmash.cli_script sourmash_plugin_branchwater 0.9.3 multisearch
sourmash.cli_script sourmash_plugin_branchwater 0.9.3 fastgather
sourmash.cli_script sourmash_plugin_branchwater 0.9.3 fastmultigather
sourmash.cli_script sourmash_plugin_branchwater 0.9.3 index
sourmash.cli_script sourmash_plugin_branchwater 0.9.3 check
sourmash.cli_script sourmash_plugin_branchwater 0.9.3 manysketch
sourmash.cli_script sourmash_plugin_branchwater 0.9.3 pairwise
sourmash.cli_script sourmash_plugin_branchwater 0.9.3 cluster

[ctb]

yep! The fastgather and fastmultigather output was finally made completely compatible with sourmash in sourmash_branchwater_plugin v0.9.5, and you have v0.9.3. So you'll need to update that! You should also consider updating sourmash to v4.8.10, although I think that is not required.

related issues:

• differences between this plugin's gather and sourmash gather sourmash_plugin_branchwater#331 (comment)

[agombolay]

Updating the versions worked for me! Thanks!

[ctb]

great, thank you for confirming!!!