unknown error in shell script - shell

Question

I have cobbled together a shell script to submit multiple jobs on a cluster, which it appears to without giving me an error message, but the output files are missing and the error log files are also empty. What the script supposed to do is 1.) make a bunch of new directories, 2.) copy four files to each (mainparams, extraparams, infile, and structurejobsubmissionfile) 3.) then submit each one to the cluster for it to run structure while changing one parameter in the mainparams file every tenth directory (that's the 's/changethis/'$k'/g' line).
Test running it on the front end gives no errors, the structure program is up to date on the cluster, and the cluster administrators don't see anything wrong. Thanks!
#!/bin/bash
reps=10
numK=10
for k in $(seq $numK);
do
for i in $(seq $reps);
do
#make folder name (ex. k4rep7)
tmpstr="k${k}rep${i}"
#echo "Making folder and filename $tmpstr"
#make the new folder
mkdir $tmpstr
#go to that folder
cd ./$tmpstr
#copy in the input files
cp ../str_in/* ./
#modify the recently copied input file here so source file remains the same
cp ./mainparams ./temp.txt
#change maxpops to current value of k and the directory for the files to the 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 so run STRUCTURE here
qsub -q fnrgenetics -l nodes=1:ppn=1,walltime=20:00:00 structurejobsubmissionfile
#go back to parent directory
cd ../
done
done

Answer 1

I can't see anything obviously wrong, but I think the place that you'll find the answer lies in better logging and better error checking. Some of the things that you're not checking that you should:
Is $tmpstr created correctly? (will fail on disk full or if permissions are not set correctly)
does str_in/ exist, and is it a directory?
does it contain files?
does it contain mainparams?
is qsub in $PATH?
does the call to qsub return an error?
You can roll an error logging function of your own, or use a package like log4bash