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sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
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KeyError:'24B' #53

Open km-bit opened 4 years ago

km-bit commented 4 years ago

Hey everyone,

I am getting a KeyError when I am running seroba on my test data. 

Traceback (most recent call last):
  File "/home/user/.local/bin/seroba", line 86, in <module>
    args.func(args)
  File "/home/user/.local/lib/python3.8/site-packages/seroba/tasks/sero_run.py", line 19, in run
    sero.run()
  File "/home/user/.local/lib/python3.8/site-packages/seroba/serotyping.py", line 479, in run
    cluster = self.serotype_cluster_dict[self.best_serotype]
KeyError: '24B'

I am not sure what it means or how to fix it. Maybe someone had the same or a similar problem ?

Thank you in advance!

eppinglen commented 4 years ago

Hi,

which Version of SeroBA are you using? Did you download the database from this git repository or did you use the build in function of SeroBA?

Best, Lennard

km-bit commented 4 years ago

Hey Lennard,

The version is 1.0.0 and I downloaded the database from the git repository. But I think the error handled itself, because yesterday my system crashed and after reinstalling seroba again from source it cannot find the command seroba. I guess I have to figure that out first.

But thank you for the quick response!

Karsten

eppinglen commented 4 years ago

The latest version of ARIBA (prepareref) seems to create an odd output of the cdhit_cluster.tsv. This leads to problems with the prediction for some serotypes. The current solution would be to downgrade ARIBA (e.g. version 2.11.1). Afterwards the database has to be rebuild.