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Description
I am running tests with a tiny database and found that the error when lemur doesn't find any matches to the fastq file in the database could be clarified.
Relevant line lemur/671
I would add a if(n_reads == 0) ; error('none of the reads match the database') response here.
Currently this is the error I get
Command error:
2025-08-26 04:32:08 PM INFO: Starting run of minimap2 at 2025-08-26 16:32:08.851068
2025-08-26 04:32:08 PM INFO: Finished running minimap2 in 140.483 ms
2025-08-26 04:32:09 PM INFO: Finished loading taxonomy in 15.223 ms
2025-08-26 04:32:09 PM INFO: Finished initializing F in 0.139 ms
2025-08-26 04:32:09 PM INFO: Finished building alignment model in 0.065 ms
2025-08-26 04:32:09 PM INFO: Finished constructing P(r|s) in 18.008 ms
Traceback (most recent call last):
File "/home/pbk1/micromamba/other-envs/env-e0dcef690672920a7ce4d792d8222b07/bin/lemur", line 901, in <module>
main()
File "/home/pbk1/micromamba/other-envs/env-e0dcef690672920a7ce4d792d8222b07/bin/lemur", line 887, in main
run.EM_complete()
File "/home/pbk1/micromamba/other-envs/env-e0dcef690672920a7ce4d792d8222b07/bin/lemur", line 672, in EM_complete
self.low_abundance_threshold = 1. / n_reads
ZeroDivisionError: float division by zero
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