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classify_wf errors out when all inputs are unclassified #576

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Zach-Sisson-1 opened this issue Mar 15, 2024 · 0 comments
Closed

classify_wf errors out when all inputs are unclassified #576

Zach-Sisson-1 opened this issue Mar 15, 2024 · 0 comments
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next version Upcoming feature/fix in staging branch.

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@Zach-Sisson-1
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The classify_ wf pipeline will error out if all input query genomes are unclassifiable as it does not produce a bac120 or ar53 summary file. However, if the input genomes contain at least one classifiable genome, then all other unclassifiable genomes get placed into the bac120 summary file and look like this:

user_genome	classification	fastani_reference	fastani_reference_radius	fastani_taxonomy	fastani_ani	fastani_af	closest_placement_reference	closest_placement_radius	closest_placement_taxonomy	closest_placement_ani	closest_placement_af	pplacer_taxonomy	classification_method	note	other_related_references(genome_id,species_name,radius,ANI,AF)	msa_percent	translation_table	red_value	warnings
00949864-6241-46e4-8c40-0efc0b7c7c55	Unclassified	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	No bacterial or archaeal marker

In this example, I ran one classifiable Archaeal genome and an unclassifiable genome which produced both the ar53 and bac120 summary files in the classify output. When running only the unclassifiable genome, I get a FileNotFound Error.

It would be nice if the bac120/ar53 summary files still get produced and take the form of the example above even if all inputs are unclassifiable instead of throwing an error.

pchaumeil added a commit that referenced this issue Apr 11, 2024
The summary files are still produces even if all genomes fail the prodigal step
pchaumeil added a commit that referenced this issue Apr 11, 2024
@pchaumeil pchaumeil added the next version Upcoming feature/fix in staging branch. label Apr 16, 2024
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