<p>I built Krakenuniq on an HPC, and I've been trying to run it on my data using the following command:</p>
<pre><code>krakenuniq --db DBDIR --threads 1 All_reads.fastq
</code></pre>
<p>This definitely isn't powerful enough to get any reasonable output, but this is just a test run. However, I got the following error:</p>
<pre><code>classify: unable to mmap ./DBDIR/database.kdb: Invalid argument
</code></pre>
<p>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.</p>

CC BY-SA 4.0
2022-05-01T17:46:42.790Z
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.
Community
CC BY-SA 4.0
2022-05-02T17:47:35.583Z
Is DBDIR in your working directory? Did you perhaps mean to write `--db ${DBDIR}`?
acvill
CC BY-SA 4.0
2022-05-03T08:13:05.293Z
That's not how it's done in the documentation, and in any case it causes its own error:
schmiggle
CC BY-SA 4.0
2022-05-03T08:20:40.357Z
`krakenuniq: unable to find --threads in $KRAKEN_DB_PATH (undefined)` DBDIR appears to be in the working directory (ls lists it there).
schmiggle
CC BY-SA 4.0
2022-05-19T07:15:36.107Z
I have run into the same issue with the default Kraken using a prebuilt database at the university HPC.
haegglund
CC BY-SA 4.0
2022-07-18T05:08:33.397Z
@schmiggle Did you ever find a solution to this? I can see the database file (for example, ./DBDIR/database.kdb) is there, but I get the same error.
isabel31672
CC BY-SA 4.0
2022-07-20T02:20:46.120Z
I switched to using Kraken2 instead because of issues like this. Didn't ever find a solution.
schmiggle
<metagenome>
Krakenuniq mmap error
# Krakenuniq mmap error

(Asked by: username_0 on 2022-05-01)

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.

**Tags:** metagenome
> **Comments:**
> **username_1**: 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.  
> **username_2**: Is DBDIR in your working directory? Did you perhaps mean to write `--db ${DBDIR}`?  
> **username_0**: That's not how it's done in the documentation, and in any case it causes its own error:  
> **username_0**: `krakenuniq: unable to find --threads in $KRAKEN_DB_PATH (undefined)` DBDIR appears to be in the working directory (ls lists it there).  
> **username_3**: I have run into the same issue with the default Kraken using a prebuilt database at the university HPC.  
> **username_4**: @schmiggle Did you ever find a solution to this? I can see the database file (for example, ./DBDIR/database.kdb) is there, but I get the same error.  
> **username_0**: I switched to using Kraken2 instead because of issues like this. Didn't ever find a solution.  

---

## 0 answers

