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fbreitwieser / krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
GNU General Public License v3.0
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db-build error: JELLYFISH_BIN: unbound variable #136

Open sepidehalamouti opened 1 year ago

sepidehalamouti commented 1 year ago

Hello I get the same krakenuniq-build (V-1.0.3) error as previous issues: krakenuniq-build --db krakenuniqdb/ --kmer-len 31 --threads 10 --taxids-for-genomes --taxids-for-sequences miniconda3/envs/krakenuniq/libexec/build_db.sh: line 64: JELLYFISH_BIN: unbound variable

Appreciate your time looking to this error. Sepideh

sepidehalamouti commented 1 year ago

resolved with adding --jellyfish-bin argument

Sabrin2020 commented 1 year ago

What was the argument added to --jellyfish-bin flag please?

douglasadamoski commented 1 year ago

I had the same error, but to solve it:

@Sabrin2020 

# Force to use jellyfish version 1.1.12 from bioconda.
# Otherwise it will instal v2xxx, it will not work
# jellyfish in condaforge is other stuff
conda install -c bioconda jellyfish=1.1.12
# Run in your conda environment, pointing to the jellyfish bin place
krakenuniq-build --build --jellyfish-bin $(type -P -a jellyfish) (..........)
apredeus commented 1 year ago

I think when you install krakenuniq from bioconda, it installs jellyfish but somehow does not know about it. Adding the --jellyfish-bin argument indeed helps.