3

I'm a bioinformatician, new in the community and quite new about working with bash-commands.

I recently encountered a very trivial error message but for me the issue is a bit complex to fix.

Briefly, when I launch a script with the qsub command (from the master node ) the job does not work and I find the following error message in the 'log' file:

Fatal error: cannot open file '/data/users/genethongandolfi/scripts/multi454.mse/multi454fasta.manip.r': No such file or directory

This sounds quite strange for me since the path to the script file called 'multi454fasta.manip.r' is correct (I already checked with the 'find' command).

I also tried to move the script into the home directory /home/genethongandolfi/scripts and the error message changes: the job runs because the system finds the script, but not the input file in the usual path /data/users/genethongandolfi/analysis/etc... . It seems to be something for which the /data/users/... path is not recognized when I launch a job.

Has QUIT--Anony-Mousse
  • 76,138
  • 12
  • 138
  • 194
Francesco Gandolfi
  • 63
  • 2
  • 5

2 Answers2

0

There are a couple of reasons why this could be the case:

  1. The file location on the slave node is different from the master
  2. The file permissions on the slave do not permit access to the file

If you can, try logging into the slave node, change to the user running the job, and check the file location and permissions.

Daniel Scott
  • 7,418
  • 5
  • 39
  • 58
-1

Had the same error for a simple c program in form of an .exe

Removing the .exe from the shell script did eventually fix it.

So instead of ./program.exe write ./program

Müsliman
  • 1