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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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KEGG reformatting regarding to #182 #273

Closed SF-Dragon closed 7 months ago

SF-Dragon commented 1 year ago

For reformatting the KEGG gene database, the provided script "emove_kegg_dups_and_rehead.py" generated the following error. I wonder how this issue can be solved.

root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/achi has a kff but no pep files root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/achl has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/acho has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/achr has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/index.html has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/index.html?C=D;O=A has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/index.html?C=D;O=D has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/index.html?C=M;O=A has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/index.html?C=M;O=D has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/index.html?C=N;O=A has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/index.html?C=N;O=D has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/index.html?C=S;O=A has no data root : ERROR The folder ftp.kegg.net/kegg/genes/organisms/index.html?C=S;O=D has no data root : CRITICAL The program will end execution because there may be errors in downloading. Traceback (most recent call last): File "/Volumes/remove_kegg_dups_and_rehead.py", line 157, in raise ValueError("System exiting see logs for why.") ValueError: System exiting see logs for why.

jrr-microbio commented 9 months ago

See this entry for help relating to KEGG database formatting: https://github.com/WrightonLabCSU/DRAM/issues/305