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/Paramecium/biaurelia/DNA/100709_IRIS_0005/s_7_1_sequence.txt /N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/DNA/100709_IRIS_0005/s_7_2_sequence.txt /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_1_sequence.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_1_sequence.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_2_sequence.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100709_IRIS_0005-s_7_2_sequence.trimmed.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10
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/Paramecium/biaurelia/DNA/100727_IRIS_0006/pbia_1_sequence.txt /N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/DNA/100727_IRIS_0006/pbia_2_sequence.txt /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_1_sequence.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_1_sequence.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_2_sequence.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/biaurelia-100727_IRIS_0006-pbia_2_sequence.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10
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/Paramecium/tredecaurelia/strain_AP38/DNA/Run_141105/209_TCCGCGAA-CCTATCCT_L001_R1_001.fastq /N/dc2/projects/paramecium/RAW_DATA/Paramecium/tredecaurelia/strain_AP38/DNA/Run_141105/209_TCCGCGAA-CCTATCCT_L001_R2_001.fastq /N/dc2/projects/marinovg/2015-01-29-P-assem/tredecaurelia-strain_AP38--Run_141105-209_TCCGCGAA-CCTATCCT_L001_R1_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/tredecaurelia-strain_AP38--Run_141105-209_TCCGCGAA-CCTATCCT_L001_R1_001.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/tredecaurelia-strain_AP38--Run_141105-209_TCCGCGAA-CCTATCCT_L001_R2_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/tredecaurelia-strain_AP38--Run_141105-209_TCCGCGAA-CCTATCCT_L001_R2_001.trimmed.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10