cd /data/images/proton2/run431/wwwSPlab/QC/trim

# trim fastqs with trimmomatic
for i in `ls ../*.fastq`
do  
echo $i; 
a=`basename $i`
echo $a
sem -j 4 --id `hostname` java  -Xmx6G -jar /data/results/tools/align/trimming/Trimmomatic-0.39/trimmomatic-0.39.jar SE -threads 2 $i  ${a%.*}.s10q20.fastq.gz SLIDINGWINDOW:10:20  2> ${a%.*}.s10q20.trim.out; 
done

for i in `ls ../*.fastq`
do  
echo $i; 
a=`basename $i`
echo $a
sem -j 4 --id `hostname` java  -Xmx6G -jar /data/results/tools/align/trimming/Trimmomatic-0.39/trimmomatic-0.39.jar SE -threads 4 $i  ${a%.*}.s10q25.fastq.gz SLIDINGWINDOW:10:25  2> ${a%.*}.s10q25.trim.out; 
done

for i in `ls ../*.fastq`
do
echo $i;
a=`basename $i`
echo $a
sem -j 4 --id `hostname` java  -Xmx6G -jar /data/results/tools/align/trimming/Trimmomatic-0.39/trimmomatic-0.39.jar SE -threads 8 $i  ${a%.*}.s10q20l20.fastq.gz SLIDINGWINDOW:10:20 MINLEN:20  2> ${a%.*}.s10q20l20.trim.out;
done



sem --id `hostname` --wait
for i in `ls *fastq.gz`
do
echo $i
/data/results/tools/qc/FastQC/fastqc $i
done