bracken-build: line 231: syntax error: unexpected end of file error

[HUANGjiadai]

bracken-build -d ../kraken2_db/

Selected Options:
kmer length = 35
read length = 100
database = ../kraken2_db/
threads = 1
kraken type = kraken2
Checking for Valid Options...
Creating database.kraken [if not found]
~/bin/bracken-build: line 231: syntax error: unexpected end of file

[alsmadin01]

Hi @HUANGjiadai,
I got the same error - did you manage to solve it?

[HUANGjiadai]

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[zxyEmily]

Hi @HUANGjiadai,
I got the same error - did you manage to solve it?

[HUANGjiadai]

这是来自QQ邮箱的假期自动回复邮件。   您好，我最近正在休假中，无法亲自回复您的邮件。我将在假期结束后，尽快给您回复。

[papanikos]

The build-kraken needs to be patched with an fi for the if [ $KRAKEN == 'kraken2' ] block to close properly.
Fixing that causes another failure in the next if block, where the exit status is checked . The check should be if [ $? == 0 ].

I see this is already on master, so depending on how you install bracken, you might not get this issue. I installed it through conda and got the error. You could try to find the build-kraken script (e.g. with the command which build-kraken) in your $PATH and replace it with the master version.