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zx0223winner / HSDFinder

a tool to predict highly similar duplicates (HSDs) in eukaryotes
MIT License
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KO database error, FileNotFoundError: [Errno 2] No such file or directory: 'KO database and its category.keg' #5

Open zx0223winner opened 1 year ago

zx0223winner commented 1 year ago

Here is the enquiry email sending from a current user which might help those who have similar concerns.

I tried for one dataset, KO database error, Suggestions please.

head user_ko.txt
g51641.t1 K17407
g32469.t1
g7221.t1
g47147.t1 K02433

python3 /home/sunn/data/softwares/HSDFinder/HSD_to_KEGG.py -i C.rhen.species.txt -k user_ko.txt -n C.rhen -o C.rhen.species.out.txt 
Traceback (most recent call last):
  File "/home/sunn/data/softwares/HSDFinder/HSD_to_KEGG.py", line 40, in <module>
    infile=open('KO database and its category.keg','r')
FileNotFoundError: [Errno 2] No such file or directory: 'KO database and its category.keg'
zx0223winner commented 1 year ago

If you check the error message, KO database and its category.keg file is missing. Make sure you download all the file from GitHub. and run the HSD_to_KEGG.py and KO database and its category.keg in the same directory. I was wondering why not use the web server which has user-friendly interface and have the python script HSD_to_KEGG.py built-in if you have tested out the heatmap drawing option.

~Xi

zx0223winner commented 1 year ago

If you check the error message, KO database and its category.keg file is missing. Make sure you download all the file from GitHub. and run the HSD_to_KEGG.py and KO database and its category.keg in the same directory. I was wondering why not use the web server which has user-friendly interface and have the python script HSD_to_KEGG.py built-in if you have tested out the heatmap drawing option.

~Xi

I was running the script from another directory, that's why HSD_to_KEGG.py unable to locate the KO db file. Problem solved.