cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-209-not-good_S97_R1_001.fastq.gz GSF816-Doak-209-not-good_S97_R2_001.fastq.gz GSF816-Doak-209-not-good_S97_R1_001.paired.fastq.gz GSF816-Doak-209-not-good_S97_R1_001.unpaired.fastq.gz GSF816-Doak-209-not-good_S97_R2_001.paired.fastq.gz GSF816-Doak-209-not-good_S97_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-223-10k_S98_R1_001.fastq.gz GSF816-Doak-223-10k_S98_R2_001.fastq.gz GSF816-Doak-223-10k_S98_R1_001.paired.fastq.gz GSF816-Doak-223-10k_S98_R1_001.unpaired.fastq.gz GSF816-Doak-223-10k_S98_R2_001.paired.fastq.gz GSF816-Doak-223-10k_S98_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-223-6k_S99_R1_001.fastq.gz GSF816-Doak-223-6k_S99_R2_001.fastq.gz GSF816-Doak-223-6k_S99_R1_001.paired.fastq.gz GSF816-Doak-223-6k_S99_R1_001.unpaired.fastq.gz GSF816-Doak-223-6k_S99_R2_001.paired.fastq.gz GSF816-Doak-223-6k_S99_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-227_S100_R1_001.fastq.gz GSF816-Doak-227_S100_R2_001.fastq.gz GSF816-Doak-227_S100_R1_001.paired.fastq.gz GSF816-Doak-227_S100_R1_001.unpaired.fastq.gz GSF816-Doak-227_S100_R2_001.paired.fastq.gz GSF816-Doak-227_S100_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-328-4-14-15_S101_R1_001.fastq.gz GSF816-Doak-328-4-14-15_S101_R2_001.fastq.gz GSF816-Doak-328-4-14-15_S101_R1_001.paired.fastq.gz GSF816-Doak-328-4-14-15_S101_R1_001.unpaired.fastq.gz GSF816-Doak-328-4-14-15_S101_R2_001.paired.fastq.gz GSF816-Doak-328-4-14-15_S101_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-K12_S102_R1_001.fastq.gz GSF816-Doak-K12_S102_R2_001.fastq.gz GSF816-Doak-K12_S102_R1_001.paired.fastq.gz GSF816-Doak-K12_S102_R1_001.unpaired.fastq.gz GSF816-Doak-K12_S102_R2_001.paired.fastq.gz GSF816-Doak-K12_S102_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-M-6k_S103_R1_001.fastq.gz GSF816-Doak-M-6k_S103_R2_001.fastq.gz GSF816-Doak-M-6k_S103_R1_001.paired.fastq.gz GSF816-Doak-M-6k_S103_R1_001.unpaired.fastq.gz GSF816-Doak-M-6k_S103_R2_001.paired.fastq.gz GSF816-Doak-M-6k_S103_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-M-7k_S104_R1_001.fastq.gz GSF816-Doak-M-7k_S104_R2_001.fastq.gz GSF816-Doak-M-7k_S104_R1_001.paired.fastq.gz GSF816-Doak-M-7k_S104_R1_001.unpaired.fastq.gz GSF816-Doak-M-7k_S104_R2_001.paired.fastq.gz GSF816-Doak-M-7k_S104_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-NiA-4-14-15_S106_R1_001.fastq.gz GSF816-Doak-NiA-4-14-15_S106_R2_001.fastq.gz GSF816-Doak-NiA-4-14-15_S106_R1_001.paired.fastq.gz GSF816-Doak-NiA-4-14-15_S106_R1_001.unpaired.fastq.gz GSF816-Doak-NiA-4-14-15_S106_R2_001.paired.fastq.gz GSF816-Doak-NiA-4-14-15_S106_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-NiA_S105_R1_001.fastq.gz GSF816-Doak-NiA_S105_R2_001.fastq.gz GSF816-Doak-NiA_S105_R1_001.paired.fastq.gz GSF816-Doak-NiA_S105_R1_001.unpaired.fastq.gz GSF816-Doak-NiA_S105_R2_001.paired.fastq.gz GSF816-Doak-NiA_S105_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-Psonn-5k_S107_R1_001.fastq.gz GSF816-Doak-Psonn-5k_S107_R2_001.fastq.gz GSF816-Doak-Psonn-5k_S107_R1_001.paired.fastq.gz GSF816-Doak-Psonn-5k_S107_R1_001.unpaired.fastq.gz GSF816-Doak-Psonn-5k_S107_R2_001.paired.fastq.gz GSF816-Doak-Psonn-5k_S107_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &
cd /N/dc2/projects/marinovg/2016-01-01-november-data; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE GSF816-Doak-Psonn-7k_S108_R1_001.fastq.gz GSF816-Doak-Psonn-7k_S108_R2_001.fastq.gz GSF816-Doak-Psonn-7k_S108_R1_001.paired.fastq.gz GSF816-Doak-Psonn-7k_S108_R1_001.unpaired.fastq.gz GSF816-Doak-Psonn-7k_S108_R2_001.paired.fastq.gz GSF816-Doak-Psonn-7k_S108_R2_001.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &