Thanks for providing such a great ancient metagenome pipe. I found a very minor issue when downloading the krakendb from https://doi.org/10.17044/scilifelab.20518251. After wget, there was a 'taxDB.' file and when I run KrakenUniq step, the error log showed:
krakenuniq --preload --db /path/to/resources/krakendb --fastq-input results/CUTADAPT_ADAPTERTRIMMING/PL0245.trimmed.fastq.gz --threads 8 --output results/KRAKENUNIQ/PL0245/sequences.krakenuniq --report-file results/KRAKENUNIQ/PL0245/krakenuniq.output --gzip-compressed --only-classified-out
NOTE: No need to use --gzip-compressed or --bzip2-compressed anymore, format is detected automatically.
NOTE: No need to use --fasta-input or --fastq-input anymore, format is detected automatically.
Taxonomy database not at /path/to/resources/krakendb/taxDB - creating it .../ path/to/tools/aMeta/resources/krakendb/taxonomy/nodes.dmp does not exist! at /path/to/tools/aMeta/.snakemake/conda/247838bd5e853115f218d1a062fdc248/bin/krakenuniq line 209.
Krakenuniq works after I changed the name of 'krakendb/taxDB.' to 'krakendb/taxDB'
Guess it could be a mismatch between the downloaded file name and the real name recognized by Krakenuniq code. Hope it would help if any of you has the same problem. Thanks!
Hi aMeta team!
Thanks for providing such a great ancient metagenome pipe. I found a very minor issue when downloading the krakendb from https://doi.org/10.17044/scilifelab.20518251. After wget, there was a 'taxDB.' file and when I run KrakenUniq step, the error log showed:
krakenuniq --preload --db /path/to/resources/krakendb --fastq-input results/CUTADAPT_ADAPTERTRIMMING/PL0245.trimmed.fastq.gz --threads 8 --output results/KRAKENUNIQ/PL0245/sequences.krakenuniq --report-file results/KRAKENUNIQ/PL0245/krakenuniq.output --gzip-compressed --only-classified-out NOTE: No need to use --gzip-compressed or --bzip2-compressed anymore, format is detected automatically. NOTE: No need to use --fasta-input or --fastq-input anymore, format is detected automatically. Taxonomy database not at /path/to/resources/krakendb/taxDB - creating it .../ path/to/tools/aMeta/resources/krakendb/taxonomy/nodes.dmp does not exist! at /path/to/tools/aMeta/.snakemake/conda/247838bd5e853115f218d1a062fdc248/bin/krakenuniq line 209.
Krakenuniq works after I changed the name of 'krakendb/taxDB.' to 'krakendb/taxDB'
Guess it could be a mismatch between the downloaded file name and the real name recognized by Krakenuniq code. Hope it would help if any of you has the same problem. Thanks!
jiajun