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Full Discussion: SGE submit script
Top Forums Shell Programming and Scripting SGE submit script Post 303006053 by una1992 on Thursday 26th of October 2017 09:59:30 AM
Old 10-26-2017
SGE submit script

Hi,

I'm trying to edit my working bash script to an SGE script in order to submit it as a job to the cluster.

Currently I have:
Code:
 
#!/bin/bash

# Perform fastqc on files in a specified directory.

for ((j=1; j <=17; j++))
do
   directory=/data4/una/batch"$j"/
   files=$""$directory"/*.fastq.gz"
   batch=$"batch_"$j""
   outfile=$""$batch"_submit_script.sh"

     echo "#!/bin/bash">>$outfile;
     echo "# Your job name">>$outfile;
     echo "# -N $batch">>$outfile;
     echo "# The job should be placed into the queue 'all.q'">>$outfile;
     echo "#$ -q all.q">>$outfile;
     echo "# Running in the current working directory">>$outfile;
     echo "#$ -cwd">>$outfile;
     echo "">>$outfile;
     echo "# Export some necessary environment variables">>$outfile;
     echo "#$ -S /bin/bash">>$outfile;
     echo "#$ -v PATH">>$outfile;
     echo "#$ -v LD_LIBRARY_PATH">>$outfile;
     echo "#$ -v PYTHONPATH">>$outfile;
     echo "# Finally, put your command here">>$outfile;
     echo "">>$outfile;
     echo "#$ for i in $files;">>$outfile;
     echo "#$ do;">>$outfile;
     echo "#$ fastqc -f fastq -o /data4/una/test/fastq/$i;">>$outfile;
     echo "#$done">>$outfile;
     echo "">>$outfile;

     qsub $outfile;
done

But I'm getting an error:
Code:
Unable to read script file because of error: ERROR! invalid option argument "-f"

But
Code:
 fastqc -f fastq -o /data4/una/test/fastq/$i

is a totally valid line in my bash script. Smilie

Thoughts?

Thanks!
 

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create_sysfile(1M)														create_sysfile(1M)

NAME
create_sysfile - create a kernel system file SYNOPSIS
[outfile] DESCRIPTION
The command creates a kernel configuration description file (system file) which can be used as input to the commands kconfig(1M) or mk_ker- nel(1M). The system file that is generated is of type version 1 (see system(4)) and is built according to the drivers required by the cur- rent system hardware. This command is intended for use during the install process when the system does not have a system file. The command uses the ioscan(1M) command to scan the system hardware and adds all drivers it can identify to run the existing hardware. If outfile is specified, the resulting system file is sent to outfile. If outfile is not specified, the output is placed in the file RETURN VALUE
Upon completion, returns with one of the following exit values: 0 Successful. 1 One or more errors were reported. DIAGNOSTICS
Errors are sent to stderr. Most of the diagnostic messages from are self-explanatory. Errors cause to halt immediately. WARNINGS
is obsolete and will be removed in a future version of HP-UX. AUTHOR
was developed by HP. SEE ALSO
ioscan(1M), kconfig(1M), mk_kernel(1M), system(4), kconfig(5). create_sysfile(1M)
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