takaram
commented
4 years ago You have to give the path of the command file instead of directory in which the command is located.
In your case, hmmsearch: /apps/free72/hmmer/3.1b2/bin/hmmsearch and parallel: /home/j/jigyasa-arora/local/parallel-20191022/src/parallel are the correct setting.
Jigyasa3
Hey @takaram
I am running the kofam_scan software giving the paths to parallel, hmmsearch to config.yml file. But I am getting the following error-
my config.yml file-
profile: /work/student/jigyasa-arora/kofamscan/db/profiles
Path to the KO list file
ko_list: /work/student/jigyasa-arora/kofamscan/db/ko_list
Path to an executable file of hmmsearch
You do not have to set this if it is in your $PATH
hmmsearch: /apps/free72/hmmer/3.1b2/bin
Path to an executable file of GNU parallel
You do not have to set this if it is in your $PATH
parallel: /home/j/jigyasa-arora/local/parallel-20191022/src
the code I am running-
$/work/student/jigyasa-arora/kofamscan/bin/kofamscan-1.1.0/exec_annotation -o 230-01-kopfam 230-01-prokka.faa
error-
Traceback (most recent call last): 8: from /work/student/jigyasa-arora/kofamscan/bin/kofamscan-1.1.0/exec_annotation:7:in
<main>' 7: from /work/student/jigyasa-arora/kofamscan/bin/kofamscan-1.1.0/lib/kofam_scan/cli.rb:21:inrun' 6: from /work/student/jigyasa-arora/kofamscan/bin/kofamscan-1.1.0/lib/kofam_scan/executor.rb:8:inexecute' 5: from /work/student/jigyasa-arora/kofamscan/bin/kofamscan-1.1.0/lib/kofam_scan/executor.rb:35:inexecute' 4: from /work/student/jigyasa-arora/kofamscan/bin/kofamscan-1.1.0/lib/kofam_scan/executor.rb:74:inrun_hmmsearch' 3: from /work/student/jigyasa-arora/kofamscan/bin/kofamscan-1.1.0/lib/kofam_scan/parallel.rb:27:inexec' 2: from /home/j/jigyasa-arora/lib/ruby/2.6.0/open3.rb:101:inpopen3' 1: from /home/j/jigyasa-arora/lib/ruby/2.6.0/open3.rb:213:inpopen_run' /home/j/jigyasa-arora/lib/ruby/2.6.0/open3.rb:213:in `spawn': Permission denied - /home/j/jigyasa-arora/local/parallel-20191022 (Errno::EACCES)