Question: (Closed) Job not running: 'No such file or directory' but the script exists
0
gravatar for fgandolfi
5.2 years ago by
fgandolfi0
France
fgandolfi0 wrote:

Hi All,

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

 

Thanks a lot in advance if somebody can help me, I don't know how to fix it..

Best,

 

Francesco

file not found shell job jobs • 4.3k views
ADD COMMENTlink written 5.2 years ago by fgandolfi0
1

Does that directory exist on the worker nodes? Presumably not. You'll have to just push an appropriate ls and/or mount command to an appropriate worker node. Note that I've run into cases where just one or two nodes didn't have a particular mount-point mounted, so keep that in mind.

ADD REPLYlink written 5.2 years ago by Devon Ryan92k

do you have the permission to work on those folders? Especially do the worker nodes have the permissions?

ADD REPLYlink written 5.2 years ago by Phil S.660

This is a discussion about the ability to run a program under a queuing system, and whilst that may be a bioinformatics program, it is not a bioinformatics *question* sorry!

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Daniel Swan13k
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