#loop-1 for 4906-gamma

cd /mainfs/home/kah1g14/raw_reads

for i in 4906-gamma-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-2 for Allen

cd /mainfs/home/kah1g14/raw_reads

for i in Allen-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-3 for Chilli

cd /mainfs/home/kah1g14/raw_reads

for i in Chilli-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-4 for Cyprus

cd /mainfs/home/kah1g14/raw_reads

for i in Cyprus-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-5 for Ebony

cd /mainfs/home/kah1g14/raw_reads

for i in Ebony-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-6 for Enchilada

cd /mainfs/home/kah1g14/raw_reads

for i in Enchilada-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-7 for Freiburg

cd /mainfs/home/kah1g14/raw_reads

for i in Freiburg-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-8 for Globulus

cd /mainfs/home/kah1g14/raw_reads

for i in Globulus-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-9 for Grawp

cd /mainfs/home/kah1g14/raw_reads

for i in Grawp-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-10 for Harry

cd /mainfs/home/kah1g14/raw_reads

for i in Harry-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-11 for Hope

cd /mainfs/home/kah1g14/raw_reads

for i in Hope-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-12 for Jane

cd /mainfs/home/kah1g14/raw_reads

for i in Jane-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-13 for Kaoota

cd /mainfs/home/kah1g14/raw_reads

for i in Kaoota-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-14 for Katie

cd /mainfs/home/kah1g14/raw_reads

for i in Katie-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-15 for Krum

cd /mainfs/home/kah1g14/raw_reads

for i in Krum-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-16 for Moody

cd /mainfs/home/kah1g14/raw_reads

for i in Moody-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-17 for NONAME

cd /mainfs/home/kah1g14/raw_reads

for i in NONAME-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-18 for Pooh

cd /mainfs/home/kah1g14/raw_reads

for i in Pooh-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-19 for RV
cd /mainfs/home/kah1g14/raw_reads

for i in RV-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-20 for Sally

cd /mainfs/home/kah1g14/raw_reads

for i in Sally-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-21 for Selma

cd /mainfs/home/kah1g14/raw_reads

for i in Selma-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-22 for Simone

cd /mainfs/home/kah1g14/raw_reads

for i in Simone-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-23 for Snape

cd /mainfs/home/kah1g14/raw_reads

for i in Snape-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-24 for Snowball

cd /mainfs/home/kah1g14/raw_reads

for i in Snowball-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-25 for Stuttgart

cd /mainfs/home/kah1g14/raw_reads

for i in Stuttgart-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-26 for Summer

cd /mainfs/home/kah1g14/raw_reads

for i in Summer-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-27 for Tabasco

cd /mainfs/home/kah1g14/raw_reads

for i in Tabasco-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-28 for Taco

cd /mainfs/home/kah1g14/raw_reads

for i in Taco-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-29 for Tibet

cd /mainfs/home/kah1g14/raw_reads

for i in Tibet-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-30 for Tigger

cd /mainfs/home/kah1g14/raw_reads

for i in Tigger-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


#loop-31 for Willie
cd /mainfs/home/kah1g14/raw_reads

for i in Willie-*.fastq

do java -jar /mainfs/scratch/kah1g14/Trimmomatic/trimmomatic-0.39.jar SE -phred33 -trimlog /mainfs/home/kah1g14/trim_logs/${i}_trim.log \
$i /mainfs/home/kah1g14/trimmed_reads/trimmed_${i} \
ILLUMINACLIP:/mainfs/scratch/kah1g14/Trimmomatic/adaptors/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:150

done


