syntax - unknown error in shell script -

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i have cobbled shell script submit multiple jobs on cluster, appears without giving me error message, output files missing , error log files empty. script supposed
1.) make bunch of new directories,
2.) copy 4 files each (mainparams, extraparams, infile, , structurejobsubmissionfile)
3.) submit each 1 cluster run structure while changing 1 parameter in mainparams file every tenth directory (that's 's/changethis/'$k'/g' line).

test running on front end gives no errors, structure program date on cluster, , cluster administrators don't see wrong. thanks!

#!/bin/bash reps=10 numk=10   k in $(seq $numk);         in $(seq $reps);                     #make folder name (ex. k4rep7)             tmpstr="k${k}rep${i}"             #echo "making folder , filename $tmpstr"             #make new folder                     mkdir $tmpstr             #go folder             cd ./$tmpstr             #copy in input files             cp ../str_in/* ./             #modify copied input file here source file remains same             cp ./mainparams ./temp.txt             #change maxpops current value of k , directory files current directory             sed -e 's/changethis/'$k'/g' -e "s:pathforrunningstructurehere:$pwd:g" ./temp.txt > ./mainparams                 #get rid of temporary file             rm ./temp.txt             #inside $i run structure here             qsub -q fnrgenetics -l nodes=1:ppn=1,walltime=20:00:00 structurejobsubmissionfile             #go parent directory             cd ../         done     done

i can't see obviously wrong, think place you'll find answer lies in better logging , better error checking. of things you're not checking should:

  1. is $tmpstr created correctly? (will fail on disk full or if permissions not set correctly)
  2. does str_in/ exist, , directory?
  3. does contain files?
  4. does contain mainparams?
  5. is qsub in $path?
  6. does call qsub return error?

you can roll error logging function of own, or use package log4bash


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