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/pentaurelia/strain_870/TS/raw_reads/130302_M00532_0028_LynchDoak527-TS22.R1.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/pentaurelia/strain_870/TS/raw_reads/130302_M00532_0028_LynchDoak527-TS22.R2.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R1.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R1.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R2.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS22.R2.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/pentaurelia/strain_870/TS/raw_reads/130302_M00532_0028_LynchDoak527-TS27.R1.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/pentaurelia/strain_870/TS/raw_reads/130302_M00532_0028_LynchDoak527-TS27.R2.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R1.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R1.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R2.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS27.R2.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/pentaurelia/strain_870/TS/raw_reads/130302_M00532_0028_LynchDoak527-TS3.R1.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/pentaurelia/strain_870/TS/raw_reads/130302_M00532_0028_LynchDoak527-TS3.R2.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R1.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R1.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R2.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS3.R2.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/pentaurelia/strain_870/TS/raw_reads/130302_M00532_0028_LynchDoak527-TS9.R1.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/pentaurelia/strain_870/TS/raw_reads/130302_M00532_0028_LynchDoak527-TS9.R2.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R1.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R1.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R2.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-TS-130302_M00532_0028_LynchDoak527-TS9.R2.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/pentaurelia/strain_870/MP/raw_reads/MP.R1.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/pentaurelia/strain_870/MP/raw_reads/MP.R2.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R1.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R1.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R2.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_870-MP-MP.R2.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/pentaurelia/strain_87E/553MP/raw_reads/130405_M01529_0005_Lynch553MP.R1.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/pentaurelia/strain_87E/553MP/raw_reads/130405_M01529_0005_Lynch553MP.R2.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553MP-130405_M01529_0005_Lynch553MP.R1.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553MP-130405_M01529_0005_Lynch553MP.R1.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553MP-130405_M01529_0005_Lynch553MP.R2.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553MP-130405_M01529_0005_Lynch553MP.R2.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/pentaurelia/strain_87E/553short/raw_reads/130405_M01529_0005_Lynch553short.R1.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/pentaurelia/strain_87E/553short/raw_reads/130405_M01529_0005_Lynch553short.R2.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553short-130405_M01529_0005_Lynch553short.R1.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553short-130405_M01529_0005_Lynch553short.R1.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553short-130405_M01529_0005_Lynch553short.R2.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/pentaurelia-strain_87E-553short-130405_M01529_0005_Lynch553short.R2.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/jenningsi/strain_M/DNA/Run_141105/M_CGGCTATG-GTACTGAC_L001_R1_001.fastq /N/dc2/projects/paramecium/RAW_DATA/Paramecium/jenningsi/strain_M/DNA/Run_141105/M_CGGCTATG-GTACTGAC_L001_R2_001.fastq /N/dc2/projects/marinovg/2015-01-29-P-assem/jenningsi-strain_M-Run_141105-M_CGGCTATG-GTACTGAC_L001_R1_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/jenningsi-strain_M-Run_141105-M_CGGCTATG-GTACTGAC_L001_R1_001.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/jenningsi-strain_M-Run_141105-M_CGGCTATG-GTACTGAC_L001_R2_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/jenningsi-strain_M-Run_141105-M_CGGCTATG-GTACTGAC_L001_R2_001.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/undecaurelia/strain_AP58/DNA/Run_141105/219-11_CGGCTATG-ATAGAGGC_L001_R1_001.fastq /N/dc2/projects/paramecium/RAW_DATA/Paramecium/undecaurelia/strain_AP58/DNA/Run_141105/219-11_CGGCTATG-ATAGAGGC_L001_R2_001.fastq /N/dc2/projects/marinovg/2015-01-29-P-assem/undecaurelia-strain_AP58-Run_141105-219-11_CGGCTATG-ATAGAGGC_L001_R1_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/undecaurelia-strain_AP58-Run_141105-219-11_CGGCTATG-ATAGAGGC_L001_R1_001.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/undecaurelia-strain_AP58-Run_141105-219-11_CGGCTATG-ATAGAGGC_L001_R2_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/undecaurelia-strain_AP58-Run_141105-219-11_CGGCTATG-ATAGAGGC_L001_R2_001.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/sonneborni/AP59/DNA/Run_141105/Psonn_CGGCTATG-AGGCGAAG_L001_R1_001.fastq /N/dc2/projects/paramecium/RAW_DATA/Paramecium/sonneborni/AP59/DNA/Run_141105/Psonn_CGGCTATG-AGGCGAAG_L001_R2_001.fastq /N/dc2/projects/marinovg/2015-01-29-P-assem/sonneborni-AP59-Run_141105-Psonn_CGGCTATG-AGGCGAAG_L001_R1_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/sonneborni-AP59-Run_141105-Psonn_CGGCTATG-AGGCGAAG_L001_R1_001.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/sonneborni-AP59-Run_141105-Psonn_CGGCTATG-AGGCGAAG_L001_R2_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/sonneborni-AP59-Run_141105-Psonn_CGGCTATG-AGGCGAAG_L001_R2_001.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/putrinum/strain_BM4-1/DNA/Run_141105/BM4-1_CGGCTATG-CCTATCCT_L001_R1_001.fastq  /N/dc2/projects/paramecium/RAW_DATA/Paramecium/putrinum/strain_BM4-1/DNA/Run_141105/BM4-1_CGGCTATG-CCTATCCT_L001_R2_001.fastq  /N/dc2/projects/marinovg/2015-01-29-P-assem/putrinum-strain_BM4-1-Run_141105-BM4-1_CGGCTATG-CCTATCCT_L001_R1_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/putrinum-strain_BM4-1-Run_141105-BM4-1_CGGCTATG-CCTATCCT_L001_R1_001.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/putrinum-strain_BM4-1-Run_141105-BM4-1_CGGCTATG-CCTATCCT_L001_R2_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/putrinum-strain_BM4-1-Run_141105-BM4-1_CGGCTATG-CCTATCCT_L001_R2_001.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/septaurelia/strain_227/DNA/Run_141105/227_TCCGCGAA-AGGCGAAG_L001_R1_001.fastq /N/dc2/projects/paramecium/RAW_DATA/Paramecium/septaurelia/strain_227/DNA/Run_141105/227_TCCGCGAA-AGGCGAAG_L001_R2_001.fastq /N/dc2/projects/marinovg/2015-01-29-P-assem/septaurelia-strain_227-Run_141105-227_TCCGCGAA-AGGCGAAG_L001_R1_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/septaurelia-strain_227-Run_141105-227_TCCGCGAA-AGGCGAAG_L001_R1_001.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/septaurelia-strain_227-Run_141105-227_TCCGCGAA-AGGCGAAG_L001_R2_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/septaurelia-strain_227-Run_141105-227_TCCGCGAA-AGGCGAAG_L001_R2_001.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/decaurelia/strain_223/DNA/Run_141105/223_CGGCTATG-GGCTCTGA_L001_R1_001.fastq /N/dc2/projects/paramecium/RAW_DATA/Paramecium/decaurelia/strain_223/DNA/Run_141105/223_CGGCTATG-GGCTCTGA_L001_R2_001.fastq /N/dc2/projects/marinovg/2015-01-29-P-assem/decaurelia-strain_223-Run_141105-223_CGGCTATG-GGCTCTGA_L001_R1_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/decaurelia-strain_223-Run_141105-223_CGGCTATG-GGCTCTGA_L001_R1_001.trimmed.unpaired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/decaurelia-strain_223-Run_141105-223_CGGCTATG-GGCTCTGA_L001_R2_001.trimmed.paired.fastq.gz /N/dc2/projects/marinovg/2015-01-29-P-assem/decaurelia-strain_223-Run_141105-223_CGGCTATG-GGCTCTGA_L001_R2_001.trimmed.unpaired.fastq.gz ILLUMINACLIP:/N/dc2/projects/marinovg/programs/Trimmomatic-0.33/adapters/NexteraPE-PE.fa:2:30:10