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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.

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  • $\begingroup$ 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

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