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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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krakenuniq-build v.0.7.3 cannot find jellyfish #74

Closed LeandroRitter closed 2 years ago

LeandroRitter commented 2 years ago

when we switched from KrakenUniq v.0.5.8 to v.0.7.3, the new version of KrakenUniq cannot automatically detect jellyfish:

(ancient_microbiome_workflow) nikolay@dell:~/WABI/A_Gotherstrom/ancient-microbiome-smk/.test$ krakenuniq-build --db resources/KrakenUniq_DB --kmer-len 21 --minimizer-len 11
Kraken build set to minimize disk writes.
Finding all library files
Found 1 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory.
Creating k-mer set (step 1 of 6)...
Using /home/nikolay/miniconda3/envs/ancient_microbiome_workflow/libexec/jellyfish-install/bin/jellyfish
Hash size not specified, using '9951131'
/home/nikolay/miniconda3/envs/ancient_microbiome_workflow/libexec/build_db.sh: line 46: /home/nikolay/miniconda3/envs/ancient_microbiome_workflow/libexec/jellyfish-install/bin/jellyfish: No such file or directory
xargs: cat: terminated by signal 13
percyfal commented 2 years ago

Yeah, I've seen this but I may have only fixed it for the github CI: see https://github.com/NBISweden/ancient-microbiome-smk/blob/main/.github/workflows/main.yaml#L72

LeandroRitter commented 2 years ago

Ok!