Bracken database error

usegalaxy.eu support
1

Hi, guys!
I have using Kraken2 and Bracken to taxonomic classification of a WGS study. In the Kraken2, I`ve used the Prebuilt Refseq indexes: PlusPF (Standard plus protozoa and fungi) (Version: 2022-06-07 - Downloaded: 2022-09-04T165121Z) database, and everything works fine. However, when I have tryed used this database for Bracken (Prebuild RefSeq indexes: PlusPF (Version: 2022-06-07, K-mer: 35, Read: 100)), an error is displayed:

Checking report file: /data/dnb09/galaxy_db/files/b/5/8/dataset_b581ea1a-7a67-4d72-b8e3-59d591bd2e0a.dat
Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__bracken@2.8/bin/est_abundance.py”, line 554, in
main()
File “/usr/local/tools/_conda/envs/__bracken@2.8/bin/est_abundance.py”, line 336, in main
k_file = open(args.kmer_distr,‘r’)
FileNotFoundError: [Errno 2] No such file or directory: ‘2022-09-04T165121Z_standard_prebuilt_pluspf_2022-06-07/database100mers.kmer_distrib’

This database is the most actualized in the Galaxy.eu server and, apparently, Bracken can`t found this database directory.

Can help me?
Regard!

2

Welcome, @Carlos-Santos

I only see one PlusPF index on the Braken tool form list at the EU server.

What am I getting wrong? Screenshot might help. Thanks!

3

Hi, @jennaj!
Thank you for the reply!
Here it’s goes some screenshots.
Thanks!

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image1285×822 45.9 KB

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image1282×829 61 KB

4

Hi @Carlos-Santos

Thanks for sharing the details.

I’ve reported the problem to the EU server administrators. Tracking ticket

For immediate use, you can try at one of the other public Galaxy servers.

Thanks for reporting the problem!

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5

@Carlos-Santos can you please try this again and let us know if it works now?

Thanks!

1 Like
6

Hi, @jennaj and @bjoern.gruening!
I have try again, and everything works fine now!

Thank you so much for all attention!
Have a nice day!

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