rawosemo

To solve this, use this flag with others, --memory-mapping So, you have something like this: kraken2 --use-names --memory-mapping --db /mnt/data/kraken_db/ --threads 8 --report kraken.report --paired R1.fastq R2.fastq > kraken.output What...

@SimonHegele is right. I ran into a similar issue, but it was solved by downloading the pre-built version of the specific database.

I indexed the bacteria database manually by downloading its prebuilt version from https://benlangmead.github.io/aws-indexes/k2. After the download is done, upload to the server, then uncompress by using: tar -xvzf $FILE_NAME Hopefully,...

@tibitoy, I have used Bracken recently. For me, I don't have the library and taxonomy directories created as well, but I was able to use Bracken since the database was...

Oh! It can't find the “nodes.dmp” file within the directory you specified. There is no “taxonomy” directory if you used the pre-built version. You might want to remove it from...