Describe the bug
I believe there may be serious errors in the default KEGG-related mapping files included in PICRUSt2.
The potentially affected files are:
description_mapfiles/KEGG_modules_info.tsv.gzdescription_mapfiles/KEGG_pathways_info.tsv.gzpathway_mapfiles/KEGG_modules_to_KO.tsvpathway_mapfiles/KEGG_pathways_to_KO.tsv
I became suspicious of this issue because methane-related KEGG modules were not detected at all, even though my samples contained methanogenic archaea. After checking the default KEGG module mapping files, I found that KEGG module connections appear to be missing or disconnected from downstream modules, at least up to M00377.
Because many researchers rely on PICRUSt2 for functional prediction, this issue could substantially affect the reliability of KEGG module and pathway predictions if it is caused by incorrect default files.
PICRUSt2 version
2.6.x
Operating system
40 threasd, 512 GB RAM
If your issue relates to either installation or running PICRUSt2, please fill in the relevant section below. Otherwise, please provide as much detail as possible about the command that you are trying to run, including screenshots or attachments of your terminal output (please do not paste terminal output directly into the text area).
Issues with running PICRUSt2
Command run
I downloaded the repository via git clone. It seems the data in the repository is incorrect.
Additional context
This issue may affect not only my own analysis but also other PICRUSt2 users who rely on the default KEGG module and pathway prediction files. Since PICRUSt2 is widely used for microbial functional prediction, I would appreciate it if the KEGG-related default mapping files could be checked and corrected as soon as possible.
Thank you for maintaining PICRUSt2.
Describe the bug
I believe there may be serious errors in the default KEGG-related mapping files included in PICRUSt2.
The potentially affected files are:
description_mapfiles/KEGG_modules_info.tsv.gzdescription_mapfiles/KEGG_pathways_info.tsv.gzpathway_mapfiles/KEGG_modules_to_KO.tsvpathway_mapfiles/KEGG_pathways_to_KO.tsvI became suspicious of this issue because methane-related KEGG modules were not detected at all, even though my samples contained methanogenic archaea. After checking the default KEGG module mapping files, I found that KEGG module connections appear to be missing or disconnected from downstream modules, at least up to
M00377.Because many researchers rely on PICRUSt2 for functional prediction, this issue could substantially affect the reliability of KEGG module and pathway predictions if it is caused by incorrect default files.
PICRUSt2 version
2.6.x
Operating system
40 threasd, 512 GB RAM
If your issue relates to either installation or running PICRUSt2, please fill in the relevant section below. Otherwise, please provide as much detail as possible about the command that you are trying to run, including screenshots or attachments of your terminal output (please do not paste terminal output directly into the text area).
Issues with running PICRUSt2
Command run
I downloaded the repository via git clone. It seems the data in the repository is incorrect.
Additional context
This issue may affect not only my own analysis but also other PICRUSt2 users who rely on the default KEGG module and pathway prediction files. Since PICRUSt2 is widely used for microbial functional prediction, I would appreciate it if the KEGG-related default mapping files could be checked and corrected as soon as possible.
Thank you for maintaining PICRUSt2.