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 https://github.com/jenniferlu717/Bracken/commit/05d695c5a8c09849c7144fa2ba9cbac81af0e166 and https://github.com/jenniferlu717/Bracken/commit/d7f63d8ff9d7d9c1bcf31d62f0ee642d6fd3d8c5.

When we conda install, we it seems that we're only getting the version https://github.com/jenniferlu717/Bracken/commit/38edbc5f7ac4e27dd90c12e9aee6ec01b248731e, 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.