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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 10 months ago

ksavhughes commented 11 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 11 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 11 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 11 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 10 months ago

Fixed in v2.0.1 #281