cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_16I-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_C026-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Canal-1I-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_M08-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_M13-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_M15-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Peniche3I-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_TRB101-4-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_256-UB2/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_256-UB2/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_256-UB2-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_258-UB4/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_258-UB4/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_258-UB4-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_31/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_31/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_31-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_379/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_44/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_44/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_44-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_45/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_45/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_45-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_562alpha/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_562alpha/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_562alpha-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_76/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_76/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_76-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_7K/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_7K/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_7K-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.biaurelia-Sample_USBL-36I1/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C023/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C023/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C023-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C033/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C033/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C033-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C065/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C083/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C104/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C119/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C119-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C131/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C131/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C131-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C147/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.caudatum-Sample_C147/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C147-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M03/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M03/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M03-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M04/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M05/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M09/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M09/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M09-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M12/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.multimicronucleatum-Sample_M12/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M12-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.octaurelia-Sample_1038/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_126/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_127/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_128/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_129/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_129-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_130/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_131/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_132/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_133/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_134/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_137/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_265/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_265/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_265-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Indo1-7I/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.sexaurelia-Sample_Moz13BIII/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_116/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_116-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_169/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_169/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_169-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_291/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_298/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_298/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_298-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_47/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_47/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_47-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_51/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_51/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_51-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_98/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_98/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_98-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_99/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A30/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_A30/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_A30-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_B/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_B/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_B-SPAdes-3.5.0-trimmed
cd /N/dc2/projects/marinovg/2015-09-07-assemblies; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_M02/reads.end1.paired.fastq.gz --pe1-2 /N/dc2/projects/marinovg/Paramecium/variation/data/P.tetraurelia-Sample_M02/reads.end2.paired.fastq.gz -t 16 -o /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_M02-SPAdes-3.5.0-trimmed