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pirovc / ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
https://pirovc.github.io/ganon/
MIT License
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Error code: -6 The number of hash functions must be > 0 and <= 5 #274

Closed ksavhughes closed 7 months ago

ksavhughes commented 8 months ago

Hi, I got this error message and I'm assuming it is because I set -s 0 to detect the optimal number of hash functions. I'm going to just try using the default (4) value but I wanted to open an issue so you all are aware of this.

build command: ganon build-custom -t 24 -x ncbi --verbose --write-info-file -c -i $db/refs/bacteria3 -d bacteria3 --level species -k 19 -w 31 -s 0 --hibf -p 0.001 --ncbi-file-info $db/refs/assembly_summaries/bacteria3_assembly_summary.txt

stderr: raptor build terminate called after throwing an instance of 'std::logic_error' what(): The number of hash functions must be > 0 and <= 5. The following command failed to run: /home/karsav1511/.conda/envs/ganon/bin/raptor build --output 'bacteria3.hibf' --threads 24 --input 'bacteria3_files/build/raptor_layout.binning.out'

Error code: -6

pirovc commented 8 months ago

Thanks for reporting. This is not documented properly, but only with --filter-type ibf the auto detection works, so for your default use case (--filter-type hibf) the n. of hashes has to be set. Either way, this is a bug and will be fixed soon.

ksavhughes commented 8 months ago

Oh ok thank you and thanks for the quick response! So do you recommend just using the default number of hashes (4)?

pirovc commented 8 months ago

4 is good. The number of hashes will change the size of your database and the classification speed, but classification results should be the same with any value.

pirovc commented 7 months ago

Fixed in v2.0.1 #281