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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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build_db.sh aborted #183

Open henr2934 opened 2 months ago

henr2934 commented 2 months ago

Hi

I have been trying to regenerate a database but keep running into the same error. I am using version 1.0.4. This is the code I have run 

krakenuniq-download --db DBDIR taxonomy
krakenuniq-download --db DBDIR --threads 10 --dust refseq/bacteria 
krakenuniq-build --db DBDIR --kmer-len 31 --threads 20 --taxids-for-genomes --taxids-for-sequences  --jellyfish-bin $jellyfishPath

This is the error. 

build_db.sh: line 46: 1484537 Aborted  (core dumped) /apps/conda/bin/jellyfish count -m 31 -s 0 -C -t 20 -o database /dev/fd/63

The database.jdb file is roughly 500GB. I have adjusted the jellyfish hashsize and rerun with the --work-on-disk option but keep running into the same error. I have access to 150-250G of RAM, am I missing something? I had previously run this code with version 0.7 and had no errors or memory issues.