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LangilleLab / microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
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Assign Taxonomy with RDP classifer #9

Closed caijian89 closed 7 years ago

caijian89 commented 7 years ago

HI Garvin！ Sorry for bothering you again.

I try to add the RDP naïve Bayesian classifier for taxonomy assignment, which included in open-reference OTU picking workflow. I had added some sentence in the clustering parameters file as following:

echo "assign_taxonomy:assignment_method rdp" >> clustering_params.txt echo "assign_taxonomy:confidence 0.8" >> clustering_params.txt

Then it warned error happened, the warning message was list as below:

*** ERROR RAISED DURING STEP: Assign taxonomy Command run was: assign_taxonomy.py -o /home/mh_user/Data/16S/anoxic/clustering//rdp_assigned_taxonomy -i /home/mh_user/Data/16S/anoxic/clustering//rep_set.fna --confidence 0.8 --id_to_taxonomy_fp /home/shared/rRNA_db/99_taxonomy_7_levels.txt --assignment_method rdp --reference_seqs_fp /home/shared/rRNA_db/99_otus_16S.fasta Command returned exit status: 2 Stdout:

Stderr Error in assign_taxonomy.py: RDP classifier is not installed or not accessible to QIIME. See install instructions here: http://qiime.org/install/install.html#rdp-install

If you need help with QIIME, see: http://help.qiime.org

Could you help with that?

Good Weekends!

Jian

gavinmdouglas commented 7 years ago

Hey again,

The RDP classifier isn’t installed on the virtual box at the moment, but you can quickly install it by downloading the source code from here: http://qiime.org/install/alternative.html http://qiime.org/install/alternative.html and by following the instructions here: http://qiime.org/install/alternative.html#rdp-jar-path-environment-variable. http://qiime.org/install/alternative.html#rdp-jar-path-environment-variable.%5C

Best,

Gavin

On Jun 24, 2017, at 11:26 PM, caijian89 notifications@github.com wrote:

HI Garvin！ Sorry for bothering you again.

I try to add the RDP naïve Bayesian classifier for taxonomy assignment, which included in open-reference OTU picking workflow. I had added some sentence in the clustering parameters file as following:

echo "assign_taxonomy:assignment_method rdp" >> clustering_params.txt echo "assign_taxonomy:confidence 0.8" >> clustering_params.txt

Then it warned error happened, the warning message was list as below:

*** ERROR RAISED DURING STEP: Assign taxonomy Command run was: assign_taxonomy.py -o /home/mh_user/Data/16S/anoxic/clustering//rdp_assigned_taxonomy -i /home/mh_user/Data/16S/anoxic/clustering//rep_set.fna --confidence 0.8 --id_to_taxonomy_fp /home/shared/rRNA_db/99_taxonomy_7_levels.txt --assignment_method rdp --reference_seqs_fp /home/shared/rRNA_db/99_otus_16S.fasta Command returned exit status: 2 Stdout:

Stderr Error in assign_taxonomy.py: RDP classifier is not installed or not accessible to QIIME. See install instructions here: http://qiime.org/install/install.html#rdp-install http://qiime.org/install/install.html#rdp-install If you need help with QIIME, see: http://help.qiime.org http://help.qiime.org/ Could you help with that?

Good Weekends!

Jian

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caijian89 commented 7 years ago

Hey, ~~ Maybe a good afternoon for you?

Thank you for your kind help, it really works as your word!

Good day

Jian