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jenniferlu717 / Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
http://ccb.jhu.edu/software/bracken/index.shtml
GNU General Public License v3.0
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bracken-build - syntax error: unexpected end of file #252

Closed nicholascdove closed 6 months ago

nicholascdove commented 6 months ago

Is there a syntax error in the braken-build script? bracken-build -d ./vir_db -t 12 # both the Bracken and Kraken2 folders are in the PATH

 >> Selected Options:
       kmer length = 35
       read length = 100
       database    = ./vir_db
       threads     = 12
       kraken type = kraken2
 >> Checking for Valid Options...
 >> Creating database.kraken [if not found]
/git/Bracken/bracken-build: line 229: syntax error: unexpected end of file

Any idea of what is going on? I looked at bracken-build, but I couldn't find a syntax error. Thanks!

nicholascdove commented 6 months ago

needs a fi on line 189.

nicholascdove commented 6 months ago

Actually, the above is not true. Not totally sure what is going on, but it looks like there is a syntax error in d26b268. Upon reverting back to 835c65b, everything works as expected.

balaram26 commented 6 months ago

this issue seem not fixed, i downloaded most recent git nd still get the issue during bracken build:

bracken-build -d new_krakne_db/ -t4 -k 20

Selected Options: kmer length = 20 read length = 100 database = new_krakne_db/ threads = 4 kraken type = kraken2 Checking for Valid Options... Creating database.kraken [if not found] ../bin/bracken-build: line 229: syntax error: unexpected end of file`