Possible build bug

[FraMatMan]

Hi! I cloned the krakenuniq repository and followed the instruction of the readme but I have an error trying to build the database.

This is th code I used krakenuniq-download --db DBDIR refseq/vertebrate_mammalian/Chromosome/species_taxid=9606 /krakenuniq-build --db DBDIR --threads 2 --jellyfish-bin /usr/bin/jellyfish

And the error:

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 /usr/bin/jellyfish Hash size not specified, using '2575692630' mv: cannot stat 'database_0': No such file or directory

A file called database (without any extension) is created but not _0 or final .kdb

Any help is appreciate! Best, Francesco

[tbazilegith]

Try to rename the BDDIR appropriately based on your genomic library of interest (e.g vertebrate_marmalian_db). Also, follow the three steps for building a DB (https://hpc.nih.gov/apps/KrakenUniq.html) Hope it helps.

[FraMatMan]

Thanks tbazilegith for the answer! I just put here the example of the readme you have in github. Unfortunately, I have already tried with different names and taxonomies, all with the same error.

What I would like to do is building a custom database with my own fastqs, but the building part fails...always with the "mv: cannot stat 'database_0': No such file or directory" error.

[FraMatMan]

Hi again! As suggested by tbazilegith, I repeated exactly the same as in https://hpc.nih.gov/apps/KrakenUniq.html but I always have the same error.

I think the possible problem come from the script build_db.sh

exe eval $JELLYFISH_BIN count -m $KRAKEN_KMER_LEN -s $KRAKEN_HASH_SIZE -C -t $KRAKEN_THREAD_CT \ -o database <( cat_library ) ... if [ -e "database_1" ] then $JELLYFISH_BIN merge -o database.jdb.tmp database_*
else mv database_0 database.jdb.tmp fi

[alekseyzimin]

This problem is due wrong version of jellyfish. You likely have jellyfish version >=2 installed, and krakenuniq expects jellyfish version 1. jellyfish has eliminated the need for merging in version 2, thus the error. I will fix the script and release an update.

@alekseyzimin