I built Krakenuniq on an HPC, and I've been trying to run it on my data using the following command:

krakenuniq --db DBDIR --threads 1 All_reads.fastq

This definitely isn't powerful enough to get any reasonable output, but this is just a test run. However, I got the following error:

classify: unable to mmap ./DBDIR/database.kdb: Invalid argument

I haven't been able to find anything about this error online. DBDIR is 1TB, which seemed huge, so I was wondering if there might have been a problem with the build, but I saw no issues in the log.

  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    May 1, 2022 at 17:46
  • $\begingroup$ Is DBDIR in your working directory? Did you perhaps mean to write --db ${DBDIR}? $\endgroup$
    – acvill
    May 2, 2022 at 17:47
  • $\begingroup$ That's not how it's done in the documentation, and in any case it causes its own error: $\endgroup$
    – schmiggle
    May 3, 2022 at 8:13
  • $\begingroup$ krakenuniq: unable to find --threads in $KRAKEN_DB_PATH (undefined) DBDIR appears to be in the working directory (ls lists it there). $\endgroup$
    – schmiggle
    May 3, 2022 at 8:20
  • $\begingroup$ I have run into the same issue with the default Kraken using a prebuilt database at the university HPC. $\endgroup$
    – haegglund
    May 19, 2022 at 7:15


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Browse other questions tagged or ask your own question.