Comments (6)
gavinmdouglas
commented on August 22, 2024
Hmm is it possible that you're inputting a table of KO abundances rather than EC abundances? The default pipeline expects EC numbers.
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JCSzamosi
commented on August 22, 2024
Yes, I am using KO abundances. Is there a flag to let it know? I don't see one documented.
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gavinmdouglas
commented on August 22, 2024
KEGG pathways aren't supported since that database is closed source. If you have a KEGG subscription you can specify the mapping file of KEGG orthologs to pathways or modules with the -m option (and turn of regrouping from gene families to reactions with --no_regroup).
You can see an example unstructured pathway mapfile in default_files/pathway_mapfiles/ec2metacyc_picrust_prokaryotic.txt
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JCSzamosi
commented on August 22, 2024
Okay, great. Thank you!
…On Mon, Jan 28, 2019 at 3:29 PM Gavin Douglas ***@***.***> wrote:
KEGG pathways aren't supported since that database is closed source. If
you have a KEGG subscription you can specify the mapping file of KEGG
orthologs to pathways or modules with the -m option (and turn of
regrouping from gene families to reactions with --no_regroup).
You can see an example unstructured pathway mapfile in
default_files/pathway_mapfiles/ec2metacyc_picrust_prokaryotic.txt
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Bioinformatician
Farncombe Metagenomics Facility
McMaster University
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JCSzamosi
commented on August 22, 2024
If I might suggest, since this is a known limitation it would be good if it
produced a more informative error message.
…On Mon, Jan 28, 2019 at 3:34 PM Gavin Douglas ***@***.***> wrote:
Closed #55 <#55>.
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Bioinformatician
Farncombe Metagenomics Facility
McMaster University
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gavinmdouglas
commented on August 22, 2024
I'll be sure to do that in the next release.
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Related Issues (20)
- UserWarning: A worker stopped while some jobs were given to the executor. HOT 14
- Error in predicting functions using fungal ITS data HOT 4
- Generating a KEGG module table from the KO table HOT 1
- place_seqs.py --ref_dir questions HOT 2
- FutureWarning / deprecation warnings HOT 1
- Error in runing picrust 2 HOT 2
- COG3512 was eliminated in the latest COG database (2020) HOT 1
- Retrieving more Fungi genomes for ITS and 18S predictions HOT 3
- Error picrust2 picrust2_pipeline.py HOT 3
- i get "1 failed, 60 passed" when i run the tests to verify the installation after installed picrust2-2.5.0 from source HOT 12
- Invalid model name error HOT 3
- PICRUSt2 with other database(e.g. cowpi) HOT 2
- warning line 341 "metagenome_pipeline.py" HOT 1
- Unable to install v2.5.1 on MackBook M1 with Monterey HOT 11
- Running PICRUSt on ITS sequences HOT 1
- Calling in ITS reference HOT 5
- Getting Reverse Complementary Seqs HOT 1
- q2-picrust2 Tutorial error_ "pro_ref.raxml_info" could not be found. HOT 1
- "Stopping - no ASV ids overlap between input FASTA and sequence abundance table" despite having exact ASV id matching. HOT 3
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