Why am I not finding any output files in the desired location? - bash

Question

I am trying to write a processing script and I am stuck at the beginning. It does not seem to be wrong but I cannot simply understand where the error is as it is completing the execution but not giving any output. Any debugging help?
#!/bin/sh
#
# Call with following arguments
# sh test.sh <output_basename> <fastq folder> <output_folder_loc>
#
#
bn=$1
floc=$2
outloc=$3
#Create an output directory
#opdir=$bn"_processed"
mkdir $outloc/$bn"_processed"
echo "output directory for fastq $outloc/$bn"_processed" ..."
fout=$outloc/$bn"_processed"
echo "$fout ..."
echo "performing assembly to create one fastq file for each read mates ..."
zcat $floc/*R1*.fastq.gz > $fout/$bn_R1.fastq
zcat $floc/*R2*.fastq.gz > $fout/$bn_R2.fastq
echo "done"
Run command:
sh test.sh S_13_O1_122 /home/vdas/data/floc/Sample_S_13_O1_122_S12919 /home/vdas/data/OC/RNA-Seq/STAR_run/mut_out
I do not see any wrong in the code and it is also runnning without error but still am not getting any output. Can anyone point me the problem?

Answer 1

First try to change two lines like this:
mkdir -p "$outloc/${bn}_processed"
fout="$outloc/${bn}_processed"
mkdir -p is good when $outloc directory doesn't exist yet.

Answer 2

you could test your arguments (the following may be only in bash, but do work when bash is invoked as /bin/sh)
var=$1
if [ ${#var} -eq 0 ]; then
echo "var is not defined" >&2
exit 1
fi
that will test that the variable has some length, you might want to test other aspects as well, for instance does
ls $floc/*R1*.fastq.gz
produce any output?

Answer 3

#!/bin/sh
#
# Call with following arguments
# sh test.sh <output_basename> <fastq folder> <output_folder_loc>
#
#
bn=$1
floc=$2
outloc=$3
#Create an output directory
#opdir=$bn"_processed"
mkdir $outloc/$bn"_processed"
echo "output directory for fastq $outloc/$bn"_processed" ..."
fout=$outloc/$bn"_processed"
echo "$fout ..."
echo "performing assembly to create one fastq file for each read mates ..."
echo $floc/*R1*.fastq.gz
echo $fout/$bn_R1.fastq
zcat -v $floc/*R1*.fastq.gz > $fout/${bn}_R1.fastq
zcat -v $floc/*R2*.fastq.gz > $fout/${bn}_R2.fastq
echo "done"
`
this may be wath you want,