Error assigning emm cluster

[ramirma]

I was running the tool to classify some Streptococcus dysgalactiae subs equisimilis (SDSE) and I got the error below. I suspect this is because the emm type found does not have a corresponding EMM cluster (these were defined only for GAS emm types) and there is no catch for this error. I am leaving also the contents of the tmp file.

Error in Stdout:

Traceback (most recent call last):
  File "/home/ramirez/miniconda3/envs/GAStools/bin/emmtyper", line 11, in <module>
    sys.exit(main())
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/emmtyper/bin/run_emmtyper.py", line 193, in main
    clusterer()
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/emmtyper/objects/clusterer.py", line 428, in __call__
    final_result = self.produce_final_result()
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/emmtyper/objects/clusterer.py", line 196, in produce_final_result
    return self.verbose_stringer()
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/emmtyper/objects/clusterer.py", line 153, in verbose_stringer
    self.list_to_string_emm_clusters(self.answers),
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/emmtyper/objects/clusterer.py", line 113, in list_to_string_emm_clusters
    string += emm.EMM(answer.type).emm_cluster
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/emmtyper/objects/emm.py", line 27, in __init__
    self.emm_cluster = self.translate_to_cluster()
  File "/home/ramirez/miniconda3/envs/GAStools/lib/python3.7/site-packages/emmtyper/objects/emm.py", line 31, in translate_to_cluster
    return cluster_translations[self.number]
KeyError: '220'

Temp file contents:

SH10487_NODE_9_length_71711_cov_24.168984_pilon	EMM220.0	100.000	180	0	0	24903	25082	1	180	9.37e-91	333	180
SH10487_NODE_9_length_71711_cov_24.168984_pilon	STC36.4	99.444	180	1	0	24903	25082	1	180	4.36e-89	327	180
SH10487_NODE_9_length_71711_cov_24.168984_pilon	STC36.0	99.444	180	1	0	24903	25082	1	180	4.36e-89	327	180
SH10487_NODE_9_length_71711_cov_24.168984_pilon	STC36.11	98.889	180	2	0	24903	25082	1	180	2.03e-87	322	180
SH10487_NODE_9_length_71711_cov_24.168984_pilon	STC36.10	98.889	180	2	0	24903	25082	1	180	2.03e-87	322	180

[andersgs]

Thank you! I’ll check it out. Any chance you can share the genome with me so I can try to reproduce the error? It would be a good test case. You can just share the relevant section too. You can reach me on Slack if you wish to share privately. I am on leave this week, but will try to get to it ASAP.

Cheers. A.