FAQ

If you are having problems with Kraken 2, please refer to the following FAQ and potential troubleshooting options. If your question is not addressed below, please submit a new github issue.

When submitting a github issue, specify

1. the command line used (kraken2-build or kraken2)
2. the database being used
3. the kraken2 version.

For github issues, it may also be helpful to provide the output of kraken2-inspect: kraken2-inspect --db MYDB > k2inspect_output.txt

Note: Use of any older kraken2 versions may contain bugs that were addressed in the newest version. If you are working with an older version, first download the newest code to test.

Updated: 08/07/2023 (page in progress)

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Table of Contents

1. Installation FAQ
2. Downloads FAQ
   • "rsync: failed to connect" error
   • rsync_from_ncbi.pl: unexpected FTP path (new server?) for na
   • Why is the masking step slow?
3. kraken2-build FAQ
   • build_db: OMP error
4. kraken2 FAQ

Installation FAQ

Downloads FAQ

"rsync: failed to connect" error

What is causing this error message?

1. The ncbi website is having problems
2. rsync is not available for your server

How do I fix this?

1. Please add the --use-ftp argument to your kraken2-build command.

rsync_from_ncbi.pl: unexpected FTP path (new server?) for na

Sometimes, NCBI releases assembly summaries that have na for FTP path instead of an actual FTP path. As we have yet to modify the download scripts to catch this error, a temporary workaround is as follows: awk -v FS='\t' '$20 != "na" {print $0}' assembly_summary.txt > new_assembly_summary.txt cp new_assembly_summary.txt assembly_summary.txt (Credit to @alxsimon)

Why is the masking step slow?

Currently, masking is single-threaded, using NCBI's dustmasker (or for protein dbs segmasker). While other steps of the build process are multi-threaded, we currently do not provide multi-threading masking.

kraken2-build FAQ

"build_db: OMP error:

Error Message: "build_db: OMP only wants you to use 4 threads"

The kraken2-build script detects how many threads your system can use. If you try to specify more threads than available, this error will print and the build will stop.

Fix: Rerun your kraken2-build command using the number of threads OMP detected.

kraken2 FAQ

Database selection

We provide a number of pre-built Kraken2 databases. Users should select a database based on the sample and computational resources available.

Users cannot add genomes to any of the pre-built databases as the whole database would need to be rebuilt.

Confidence Score

The authors of Kraken2 use the default confidence score of 0 for our own projects, preferring to use the minimizer score for elimination of potential contamination. However, a confidence score may be useful depending on the use case. Please see Wright et al. for more details:

• Wright, Robyn J., Andrè M. Comeau, and Morgan G. I. Langille. 2023. “From Defaults to Databases: Parameter and Database Choice Dramatically Impact the Performance of Metagenomic Taxonomic Classification Tools.” Microbial Genomics 9 (3). https://doi.org/10.1099/mgen.0.000949.

This paper is an independent study of the accuracy of Kraken2 and MetaPhlAn3 using various databases and parameters.