Open queirozhanna opened 7 months ago
Hi @queirozhanna,
did you
Download KOfam database from ftp://ftp.genome.jp/pub/db/kofam/ and decompress it. You will get profile HMMs in profiles/ directory and ko_list.
If so specify the path with
exec_annotation -o output.tsv input.fasta -p /path/to/your/profiles/directory/ -k /path/to/your/ko_list
Cheers Bastian
thank you a lot! @bheimbu
Hello,
I've tried the command the tutorial suggests
$ ./exec_annotation -o output.tsv input.fasta
but I when I run it on my terminal, I get the message "Error: KO list not given"I've also tried this command:
$ ./exec_annotation -p /path/to/profiles/directory -k /path/to/ko_list/directory -o output.tsv input.fasta --cpu=8
but I get this message
/home/hanna/kofamscan/bin/kofam_scan-1.3.0/lib/kofam_scan/ko.rb:11:in
gets': Is a directory @ io_fillbuf - fd:5 /home/hanna/kofamscan/db/ (Errno::EISDIR) from /home/hanna/kofamscan/bin/kofam_scan-1.3.0/lib/kofam_scan/ko.rb:11:inparse' from /home/hanna/kofamscan/bin/kofam_scan-1.3.0/lib/kofam_scan/executor.rb:80:in
block in parse_ko' from /home/hanna/kofamscan/bin/kofam_scan-1.3.0/lib/kofam_scan/executor.rb:80:inopen' from /home/hanna/kofamscan/bin/kofam_scan-1.3.0/lib/kofam_scan/executor.rb:80:in
parse_ko' from /home/hanna/kofamscan/bin/kofam_scan-1.3.0/lib/kofam_scan/executor.rb:22:inexecute' from /home/hanna/kofamscan/bin/kofam_scan-1.3.0/lib/kofam_scan/executor.rb:8:in
execute' from /home/hanna/kofamscan/bin/kofam_scan-1.3.0/lib/kofam_scan/cli.rb:21:inrun' from ./exec_annotation:7:in
I've searched for a way to solve this issue but none of the solutions worked. 😣