#!/bin/bash

cd “#{jobs_dir}/../” echo “#{script_name} is starting at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs” #{samp_options.join(“ \n ”)} \

#{run_local}

# check file size less than 1MB

if [ $(stat –printf=“%s” “#{output}”) -le 1024000 ] then

echo "Error with output."
exit 100

fi

check STDOUT has correct termination string HASENDING=$(tail -5 #{jobs_dir}/#{script_name}.err | grep “ sequences have been processed.”)

if [ -n “$HASENDING” ] then

echo "OUTPUT ok."

else

#echo " empty variable"
echo "Improper stdout termination"
exit 100

fi

check for correct number of sequences processed, based on fastq records

PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep “ sequences have been processed.” | grep -o “[0-9]\+”)

echo “checking stdout file: ” #{jobs_dir}/#{script_name}.err echo “bwa processed” $PROCESSED echo “#{script_name} is finished at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs”