Question: kmergenie can not execute on a file because directory not exist?
0
gravatar for pbigbig
2.3 years ago by
pbigbig180
United States
pbigbig180 wrote:

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 !

kmergenie • 1.4k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by pbigbig180
1

Hi! Did you run "make" in kmergenie folder? What's the output of "make check? Perhaps.. the "no such file or directory" indicates that the specialk executable is missing, not the data file :)

ADD REPLYlink written 2.3 years ago by Rayan Chikhi1.2k

Thanks, here is the result:

[igr.ntphuong@rock kmergenie-1.6982]$ ls
CHANGELOG  __init__.py  kmergenie  LICENSE  main.cpp  makefile  minia  README  scripts  third_party  wrapper.py
[igr.ntphuong@rock kmergenie-1.6982]$ make
g++ -o minia/Pool.o -c minia/Pool.cpp -O4 -pthread  -D_largeint -DKMER_PRECISION=4
Assembler messages:
Fatal error: can't create minia/Pool.o: Permission denied
make: *** [minia/Pool.o] Error 1
[igr.ntphuong@rock kmergenie-1.6982]$ sudo make
[sudo] password for igr.ntphuong:
Sorry, user igr.ntphuong is not allowed to execute '/usr/bin/make' as root on rock.vaist.vn.
[igr.ntphuong@rock kmergenie-1.6982]$

Maybe the administrator did not install kmergenie regularly?

 

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by pbigbig180
1

You don't need to do "sudo". A simple "make" is sufficient. But apparently, Pool.o was already compiled by root. So you need to type:

sudo rm *.o

sudo rm minia/*.o

make

ADD REPLYlink written 2.3 years ago by Rayan Chikhi1.2k

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).

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by pbigbig180

What was the output of the commands I gave you?

ADD REPLYlink written 2.3 years ago by Rayan Chikhi1.2k

Here they are:
 

[igr.ntphuong@rock apps]$ cd kmergenie-1.6982
[igr.ntphuong@rock kmergenie-1.6982]$ ls
CHANGELOG  __init__.py  kmergenie  LICENSE  main.cpp  makefile  minia  README  scripts  third_party  wrapper.py
[igr.ntphuong@rock kmergenie-1.6982]$ sudo rm *.o
[sudo] password for igr.ntphuong:
Sorry, user igr.ntphuong is not allowed to execute '/bin/rm *.o' as root on rock.vaist.vn.
[igr.ntphuong@rock kmergenie-1.6982]$ sudo rm /minia/*.o
[sudo] password for igr.ntphuong:
Sorry, user igr.ntphuong is not allowed to execute '/bin/rm ./minia/*.o' as root on rock.vaist.vn.
[igr.ntphuong@rock kmergenie-1.6982]$ make
g++ -o minia/Pool.o -c minia/Pool.cpp -O4 -pthread  -D_largeint -DKMER_PRECISION=4
Assembler messages:
Fatal error: can't create minia/Pool.o: Permission denied
make: *** [minia/Pool.o] Error 1

 

 

ADD REPLYlink written 2.3 years ago by pbigbig180

Thanks. I see. Indeed, you could contact your system administrator about removing the *.o files in there.

 

ADD REPLYlink written 2.3 years ago by Rayan Chikhi1.2k
1

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 my merged.fq.gz (in /export/home/igr.ntphuong/fastq), From here, I can rm ./minia/*.o liberately (didnt need sudo), then "make" as you suggested and I could run ./kmergenie normally.

(But I remember that at some point, I have to change to permission of ./fastq folder to 777 to be able to perform "make")

ADD REPLYlink written 2.3 years ago by pbigbig180
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