Issue when I run the analysis

[queirozhanna]

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:in parse' 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:in open' 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:in execute' 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:in run' from ./exec_annotation:7:in

'`

I've searched for a way to solve this issue but none of the solutions worked. 😣

[bheimbu]

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

[queirozhanna]

thank you a lot! @bheimbu