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I'm using "qsub" to submit a script to the cluster. My command is this:

qsub -cwd -e err -o out ./ps1.R file1 file2 file3 file4 file5

However, the err file keeps saying:

/farmshare/software/free/oge/2011.11p1/FStrusty/spool/barley03/job_scripts/726885: line 1: syntax error near unexpected token `'hi''

/farmshare/software/free/oge/2011.11p1/FStrusty/spool/barley03/job_scripts/726885: line 1: `print('hi')'

In my script the first three lines say this: 

print('hi')
args = commandArgs(TRUE)
table = read.table(args[1], header = T)

I initially also had #!/usr/bin/Rscript at the top. But it had the same error then too. Does anyone know what the problem might be?

Maheetha Bharadwaj
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  • I had similar issues when my pbs jobscript was not executable: for some reason the shell attempted to execute the output of my .profile. Maybe you ran into the same problem. I am using torque/moab and write pbs jobscripts for running the programs, I don't know about your case. – Ott Toomet Jan 26 '16 at 05:01
  • Thank you, I'll look into it. – Maheetha Bharadwaj Jan 26 '16 at 20:30

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