cd /N/dc2/projects/marinovg/2016-04-04-2014-11-05-data-SPAdes-assemblies; java -Xmx256m -classpath /N/dc2/projects/marinovg/programs/Trimmomatic-0.33/trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R1_001.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R1_002.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R1_003.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R1_004.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R1_005.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R1_006.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R1_007.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R2_001.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R2_002.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R2_003.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R2_004.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R2_005.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R2_006.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Runs/141105/dual_index/Sample_A39/A39_TCCGCGAA-TAATCTTA_L001_R2_007.fastq.gz Sample_A39.read1.paired.fastq.gz Sample_A39.read1.unpaired.fastq.gz Sample_A39.read2.paired.fastq.gz Sample_A39.read2.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10 &