Using centrifuge premade (.cf) database

khyox / recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

http://www.recentrifuge.org

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Using centrifuge premade (.cf) database #12

Closed benkraj closed 5 years ago

benkraj commented 5 years ago

Hi-

I'm looking to use recentrifuge with an existing pre-built nt centrifuge database (i.e. files nt.1.cf, nt.2.cf, nt.3.cf, and nt.4.cf). From here you seem to point to being able to use this directly. Am I missing a step to get the .dmp files from this cf database?

Thanks, Ben

benkraj commented 5 years ago

Also, I realize this seems similar to this issue, but I wasn't able to resolve it directly based on that info.

khyox commented 5 years ago

Hi Ben,

Short-answer: Just proceed following the installation instructions and use retaxdump as directed in the installation instructions.
Long-answer: In case a custom Centrifuge database I suggest using the NCBI taxdump files that were used to build such database (or a more recent release). But, in case of a pre-built nt centrifuge database, I would use any recent version of the NCBI taxdump files. This includes the ones retrieved by retaxdump when you follow the Recentrifuge installation instructions. In case of an important mismatch between the contents of the NCBI taxdump databases used by the classifier and Recentrifuge, you will get warning messages in the console. Please read the Troubleshooting section for details.

benkraj commented 5 years ago

Ok great. Thanks for your help Jose.

benkraj commented 5 years ago

Also as a note, I was having an issue with the retaxdump script. `(centrifuge) [krajacichbj@cn3286 centrifugedb]$ python retaxdump

=-= retaxdump =-= v0.28.7 - Mar 2019 =-= by Jose Manuel Martí =-=

Downloading taxdmp.zip from NCBI FTP... PROBLEM! Retrying with HTTPS... OK! Traceback (most recent call last): File "retaxdump", line 126, in main() File "retaxdump", line 114, in main filezip = ZipFile(ZIPFILE) File "/data/krajacichbj/conda/envs/centrifuge/lib/python3.6/zipfile.py", line 1131, in init self._RealGetContents() File "/data/krajacichbj/conda/envs/centrifuge/lib/python3.6/zipfile.py", line 1198, in _RealGetContents raise BadZipFile("File is not a zip file") zipfile.BadZipFile: File is not a zip file `

I manually downloaded it from the linked ftp and just pointed the rcf -n to the files which made it work fine. It 100% may be an issue with my configuration, but thought I'd drop a note in case it's something else.

khyox commented 5 years ago

Hi Ben. Thanks for the feedback! Regarding your last problem, I have tested retaxdump locally and also relaunched the Travis CI build for the last release (0.28.7), and all seem fine (https://travis-ci.org/khyox/recentrifuge/builds/503390908). I guess it could be an issue not related to Recentrifuge, perhaps some network trouble. Thanks.