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takaram / kofam_scan

CLI tool to annotate genes with KOfam
https://www.genome.jp/tools/kofamkoala/
MIT License
66 stars 11 forks source link

The set of E-value (-E) did not work. #20

Open Jiulong-Zhao opened 3 years ago

Jiulong-Zhao commented 3 years ago

Hi, kofam_scan_colleagues: Recently, I run the kofam_scan software using the following command line: exec_annotation -o 5k+_assembled_hits_to_vHMMs_ko.txt 5k+_all_assemblied_contigs.part_329_prot.fasta -k ~/database/kofam/ko_list -p ~/database/kofam/profiles/ -E 0.00001 --cpu 5 But, it seems like the "-E 0.00001" did not work. The result file contained many hits which have the e-value higher than 0.00001. I tried "-E 0.00001" and "-E 1.0e-05", but both can not work. My input file was attached. Thank you all and look forward to your reply. 5k+_all_assemblied_contigs.part_329_prot.txt

David-Madrigal commented 1 year ago

I'm having this exact same issue. Modifying the e-value do not change anything in the output file…

Did you manage to solve it somehow?

francesco-ricci commented 1 year ago

I am looking for an answer to this question too