conda bracken error, help me plz........

[DaHye0205]

I installed bracken using the command "conda install bracken" in the conda environment.
I finished analyzing the nanopore 16S metagenome and want to do further analysis with bracken.
I created the read_length.txt file myself. (300, 1500, 1600)

But I keep getting an error.

(OKHEE3.7) user@ubuntu:~/anaconda3$ bracken-build -d /data/kraken2_db -t 24 -l /home/user/anaconda3/read_lengths.txt

Selected Options:
kmer length = 35
read length = /home/user/anaconda3/read_lengths.txt
database = /data/kraken2_db
threads = 24
kraken type = kraken2
Checking for Valid Options...
Creating database.kraken [if not found]
/home/user/anaconda3/envs/OKHEE3.7/bin/bracken-build: line 231: syntax error: unexpected end of file
(OKHEE3.7) user@ubuntu:~/anaconda3$

I updated the conda environment and tried reinstalling.
What's the problem?
Is it difficult to operate in conda?

I downloaded kraken2 db with the command below and it works fine.
"kraken2-build --standard --db /data/kraken2_db --threads 24"

[sterrettJD]

Hey @jenniferlu717 - we (@jboconnor13 + me) have also dealt with this issue, which we addressed by manually updating bracken-build based on what you did in 05d695c and d7f63d8.

When we conda install, we it seems that we're only getting the version 38edbc5, which looks like the 3.0 release.

Are the last 2 commits not getting pushed to conda? Any chance we could get a 3.1 release pushed to conda to address this issue?

Thanks!

[DaHye0205]

The problem has been solved. Thank you.

[sterrettJD]

@DaHye0205 did something you did solve the issue, or is the conda installation now working for you?

[DaHye0205]

It works fine, thank you.

[joshua6061]

@sterrettJD Thanks for the pointer. Issue solved by manually updating.