kmergenie can not execute on a file because directory not exist?
Hi,
I am trying to run kmergenie installed on a server, but it always showed errors:
Execution of specialk failed: [Errno 2] No such file or directory
I tried to cd to kmergenie directory and run ./kmergenie <path to merged.fq.gz file>
or cd to file directory and run kmergenie by <path to kmergenie>/kmergenie merged.fq.gz, but none of them work
Here is my entered script:
[igr.ntphuong@rock kmergenie-1.6982]$ cd ~
[igr.ntphuong@rock ~]$ ls
bio fastq new
[igr.ntphuong@rock ~]$ cd fastq
[igr.ntphuong@rock fastq]$ ls
merged.fq.gz
[igr.ntphuong@rock fastq]$ pwd
/export/home/igr.ntphuong/fastq
[igr.ntphuong@rock fastq]$ cd /share/apps/kmergenie-1.6982
[igr.ntphuong@rock kmergenie-1.6982]$ ./kmergenie /export/home/igr.ntphuong/fastq/merged.fq.gz
running histogram estimation
Execution of specialk failed: [Errno 2] No such file or directory
[igr.ntphuong@rock fastq]$ /share/apps/kmergenie-1.6982/kmergenie merged.fq.gz
running histogram estimation
Execution of specialk failed: [Errno 2] No such file or directory
Could you please help me find out the reason?
Thanks a lot!
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Hi! Did you run
makein kmergenie folder? What's the output ofmake check? Perhaps.. the "no such file or directory" indicates that the specialk executable is missing, not the data file :)Thanks, here is the result:
Maybe the administrator did not install kmergenie regularly?
You don't need to do
sudo. A simplemakeis sufficient. But apparently,Pool.owas already compiled by root. So you need to type:Thank you Rayan,
I tried it out but it doesn't work, maybe I should contact the administrator so they could compile the program again (with sudo privilige).
What was the output of the commands I gave you?
Here they are:
Thanks. I see. Indeed, you could contact your system administrator about removing the
*.ofiles in there.Thank you Rayan, I have fixed the problem by myself!
I copied all the content inside
/share/apps/kmergenie-1.6982/to the folder containing mymerged.fq.gz(in/export/home/igr.ntphuong/fastq), From here, I canrm ./minia/*.o(didn't need sudo), thenmakeas you suggested and I could run./kmergenienormally.(But I remember that at some point, I have to change to permission of
./fastqfolder to 777 to be able to performmake)