MLST tool output unexpected.

Dear EU Galaxy community,

The MLST tool is not producing the expected output. The output file is blank while the job is described to be sucessfully completed (Green)

Kindly have a look. :smile:

Thank you!

Hi @Shreyash_04

This tool might produce valid blank results if the query didn’t match anything in the databases it is searching against.

Have you confirmed that the query term(s) should find a match? Remember that computers will match on exact terms that are caseSensitive.

If you would like some help with troubleshooting, you are welcome to share your data. See the banner here or directly →

A really small example of a failed match, that should be match, is how we could also confirm and report some tool problem if that turns out to be what is going on. You can share any external links here, too (expected result). :slight_smile:

Hello @jennaj ,

Thank you for the detailed solution. I am not sure how should we troubleshoot it. The job info has a following message in job error (Job shows green).

I attempted to run the tool on an E.coli genome, it worked and gave the following output.

Probably the MLST tool reference database does not have the information on the species of genome I have as query.

Can you please direct me to tools that can be used for species or taxonomic profiling of de-novo assembled genomes. I tried Kraken 2 on the sequence reads, but would like to have a tool that predicts the taxonomy based on assembled genome.

Thank you for your valuable time and attention to the matter. :slight_smile:

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The message from the tool stated what seems to be a data content message about the query instead “No novel intact alleles”. That is in the original code here mlst/bin/mlst at 157c519329d666dc2129d960a076528e54788a3c · tseemann/mlst · GitHub

So … I am not sure if that can result if the target species doesn’t exist at all in the references … but tools sometimes do odd yet 'logical" things when not supplied with exactly what they are expecting, and I could see that message meaning: no baseline (first column in the output), so no comparison results (other columns, which results in don’t even bother creating a new data line in the output = empty “successful” job)! :slight_smile:.

For another metagenomics annotation tool, maybe try MetaPhlAn?

For genome annotation (general), see the tool group Annotation. And, tutorials are here (also linked at the bottom of some tool forms, if you search that way) Genome Annotation / Tutorial List → Annotation of prokaryotic genomes.

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