cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M10/Sample_M10.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M10/Sample_M10.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M10-Sample_M10.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M12/Sample_M12.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M12/Sample_M12.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M12-Sample_M12.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M13/Sample_M13.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M13/Sample_M13.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M13-Sample_M13.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M14/Sample_M14.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M14/Sample_M14.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M14-Sample_M14.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M15/Sample_M15.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M15/Sample_M15.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M15-Sample_M15.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M17/Sample_M17.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M17/Sample_M17.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M17-Sample_M17.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M18/Sample_M18.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M18/Sample_M18.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M18-Sample_M18.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M2/Sample_M2.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M2/Sample_M2.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M2-Sample_M2.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M20/Sample_M20.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M20/Sample_M20.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M20-Sample_M20.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M23/Sample_M23.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M23/Sample_M23.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M23-Sample_M23.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M24/Sample_M24.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M24/Sample_M24.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M24-Sample_M24.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M25/Sample_M25.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M25/Sample_M25.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M25-Sample_M25.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M26/Sample_M26.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M26/Sample_M26.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M26-Sample_M26.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M27/Sample_M27.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M27/Sample_M27.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M27-Sample_M27.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M28/Sample_M28.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M28/Sample_M28.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M28-Sample_M28.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M29/Sample_M29.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M29/Sample_M29.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M29-Sample_M29.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M3/Sample_M3.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M3/Sample_M3.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M3-Sample_M3.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M30/Sample_M30.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M30/Sample_M30.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M30-Sample_M30.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M31/Sample_M31.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M31/Sample_M31.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M31-Sample_M31.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M32/Sample_M32.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M32/Sample_M32.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M32-Sample_M32.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M33/Sample_M33.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M33/Sample_M33.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M33-Sample_M33.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M34/Sample_M34.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M34/Sample_M34.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M34-Sample_M34.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M35/Sample_M35.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M35/Sample_M35.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M35-Sample_M35.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M38/Sample_M38.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M38/Sample_M38.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M38-Sample_M38.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M4/Sample_M4.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M4/Sample_M4.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M4-Sample_M4.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M40/Sample_M40.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M40/Sample_M40.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M40-Sample_M40.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M41/Sample_M41.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M41/Sample_M41.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M41-Sample_M41.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M42/Sample_M42.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M42/Sample_M42.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M42-Sample_M42.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M43/Sample_M43.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M43/Sample_M43.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M43-Sample_M43.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M44/Sample_M44.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M44/Sample_M44.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M44-Sample_M44.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M46/Sample_M46.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M46/Sample_M46.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M46-Sample_M46.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M48/Sample_M48.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M48/Sample_M48.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M48-Sample_M48.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M5/Sample_M5.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M5/Sample_M5.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M5-Sample_M5.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M9/Sample_M9.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M9/Sample_M9.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150116-Sample_M9-Sample_M9.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M10/Sample_M10.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M10/Sample_M10.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M10-Sample_M10.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M12/Sample_M12.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M12/Sample_M12.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M12-Sample_M12.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M13/Sample_M13.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M13/Sample_M13.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M13-Sample_M13.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M14/Sample_M14.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M14/Sample_M14.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M14-Sample_M14.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M15/Sample_M15.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M15/Sample_M15.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M15-Sample_M15.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M17/Sample_M17.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M17/Sample_M17.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M17-Sample_M17.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M18/Sample_M18.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M18/Sample_M18.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M18-Sample_M18.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M2/Sample_M2.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M2/Sample_M2.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M2-Sample_M2.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M20/Sample_M20.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M20/Sample_M20.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M20-Sample_M20.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M23/Sample_M23.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M23/Sample_M23.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M23-Sample_M23.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M24/Sample_M24.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M24/Sample_M24.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M24-Sample_M24.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M25/Sample_M25.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M25/Sample_M25.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M25-Sample_M25.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M26/Sample_M26.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M26/Sample_M26.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M26-Sample_M26.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M27/Sample_M27.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M27/Sample_M27.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M27-Sample_M27.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M28/Sample_M28.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M28/Sample_M28.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M28-Sample_M28.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M29/Sample_M29.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M29/Sample_M29.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M29-Sample_M29.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M3/Sample_M3.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M3/Sample_M3.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M3-Sample_M3.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M30/Sample_M30.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M30/Sample_M30.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M30-Sample_M30.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M31/Sample_M31.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M31/Sample_M31.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M31-Sample_M31.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M32/Sample_M32.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M32/Sample_M32.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M32-Sample_M32.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M33/Sample_M33.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M33/Sample_M33.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M33-Sample_M33.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M34/Sample_M34.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M34/Sample_M34.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M34-Sample_M34.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M35/Sample_M35.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M35/Sample_M35.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M35-Sample_M35.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M38/Sample_M38.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M38/Sample_M38.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M38-Sample_M38.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M4/Sample_M4.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M4/Sample_M4.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M4-Sample_M4.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M40/Sample_M40.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M40/Sample_M40.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M40-Sample_M40.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M41/Sample_M41.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M41/Sample_M41.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M41-Sample_M41.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M42/Sample_M42.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M42/Sample_M42.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M42-Sample_M42.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M43/Sample_M43.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M43/Sample_M43.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M43-Sample_M43.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M46/Sample_M46.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M46/Sample_M46.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M46-Sample_M46.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M48/Sample_M48.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M48/Sample_M48.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M48-Sample_M48.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M5/Sample_M5.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M5/Sample_M5.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M5-Sample_M5.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M9/Sample_M9.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M9/Sample_M9.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150204-Sample_M9-Sample_M9.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M10/Sample_M10.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M10/Sample_M10.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M10-Sample_M10.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M12/Sample_M12.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M12/Sample_M12.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M12-Sample_M12.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M13/Sample_M13.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M13/Sample_M13.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M13-Sample_M13.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M14/Sample_M14.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M14/Sample_M14.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M14-Sample_M14.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M15/Sample_M15.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M15/Sample_M15.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M15-Sample_M15.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M17/Sample_M17.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M17/Sample_M17.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M17-Sample_M17.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M18/Sample_M18.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M18/Sample_M18.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M18-Sample_M18.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M2/Sample_M2.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M2/Sample_M2.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M2-Sample_M2.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M20/Sample_M20.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M20/Sample_M20.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M20-Sample_M20.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M23/Sample_M23.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M23/Sample_M23.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M23-Sample_M23.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M24/Sample_M24.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M24/Sample_M24.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M24-Sample_M24.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M25/Sample_M25.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M25/Sample_M25.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M25-Sample_M25.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M26/Sample_M26.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M26/Sample_M26.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M26-Sample_M26.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M27/Sample_M27.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M27/Sample_M27.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M27-Sample_M27.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M28/Sample_M28.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M28/Sample_M28.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M28-Sample_M28.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M29/Sample_M29.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M29/Sample_M29.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M29-Sample_M29.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M3/Sample_M3.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M3/Sample_M3.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M3-Sample_M3.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M30/Sample_M30.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M30/Sample_M30.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M30-Sample_M30.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M31/Sample_M31.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M31/Sample_M31.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M31-Sample_M31.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M32/Sample_M32.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M32/Sample_M32.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M32-Sample_M32.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M33/Sample_M33.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M33/Sample_M33.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M33-Sample_M33.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M34/Sample_M34.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M34/Sample_M34.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M34-Sample_M34.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M35/Sample_M35.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M35/Sample_M35.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M35-Sample_M35.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M38/Sample_M38.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M38/Sample_M38.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M38-Sample_M38.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M4/Sample_M4.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M4/Sample_M4.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M4-Sample_M4.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M40/Sample_M40.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M40/Sample_M40.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M40-Sample_M40.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M41/Sample_M41.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M41/Sample_M41.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M41-Sample_M41.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M42/Sample_M42.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M42/Sample_M42.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M42-Sample_M42.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M43/Sample_M43.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M43/Sample_M43.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M43-Sample_M43.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M46/Sample_M46.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M46/Sample_M46.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M46-Sample_M46.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M48/Sample_M48.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M48/Sample_M48.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M48-Sample_M48.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M5/Sample_M5.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M5/Sample_M5.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M5-Sample_M5.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M9/Sample_M9.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M9/Sample_M9.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_A-Sample_M9-Sample_M9.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M10/Sample_M10.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M10/Sample_M10.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M10-Sample_M10.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M12/Sample_M12.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M12/Sample_M12.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M12-Sample_M12.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M13/Sample_M13.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M13/Sample_M13.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M13-Sample_M13.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M14/Sample_M14.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M14/Sample_M14.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M14-Sample_M14.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M15/Sample_M15.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M15/Sample_M15.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M15-Sample_M15.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M17/Sample_M17.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M17/Sample_M17.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M17-Sample_M17.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M18/Sample_M18.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M18/Sample_M18.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M18-Sample_M18.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M2/Sample_M2.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M2/Sample_M2.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M2-Sample_M2.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M20/Sample_M20.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M20/Sample_M20.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M20-Sample_M20.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M23/Sample_M23.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M23/Sample_M23.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M23-Sample_M23.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M24/Sample_M24.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M24/Sample_M24.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M24-Sample_M24.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M25/Sample_M25.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M25/Sample_M25.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M25-Sample_M25.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M26/Sample_M26.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M26/Sample_M26.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M26-Sample_M26.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M27/Sample_M27.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M27/Sample_M27.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M27-Sample_M27.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M28/Sample_M28.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M28/Sample_M28.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M28-Sample_M28.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M29/Sample_M29.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M29/Sample_M29.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M29-Sample_M29.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M3/Sample_M3.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M3/Sample_M3.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M3-Sample_M3.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M30/Sample_M30.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M30/Sample_M30.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M30-Sample_M30.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M31/Sample_M31.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M31/Sample_M31.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M31-Sample_M31.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M32/Sample_M32.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M32/Sample_M32.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M32-Sample_M32.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M33/Sample_M33.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M33/Sample_M33.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M33-Sample_M33.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M34/Sample_M34.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M34/Sample_M34.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M34-Sample_M34.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M35/Sample_M35.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M35/Sample_M35.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M35-Sample_M35.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M38/Sample_M38.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M38/Sample_M38.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M38-Sample_M38.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M4/Sample_M4.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M4/Sample_M4.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M4-Sample_M4.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M40/Sample_M40.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M40/Sample_M40.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M40-Sample_M40.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M41/Sample_M41.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M41/Sample_M41.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M41-Sample_M41.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M42/Sample_M42.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M42/Sample_M42.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M42-Sample_M42.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M43/Sample_M43.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M43/Sample_M43.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M43-Sample_M43.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M46/Sample_M46.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M46/Sample_M46.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M46-Sample_M46.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M48/Sample_M48.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M48/Sample_M48.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M48-Sample_M48.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M5/Sample_M5.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M5/Sample_M5.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M5-Sample_M5.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M9/Sample_M9.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M9/Sample_M9.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150206_B-Sample_M9-Sample_M9.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M10/Sample_M10.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M10/Sample_M10.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M10-Sample_M10.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M12/Sample_M12.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M12/Sample_M12.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M12-Sample_M12.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M13/Sample_M13.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M13/Sample_M13.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M13-Sample_M13.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M14/Sample_M14.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M14/Sample_M14.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M14-Sample_M14.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M15/Sample_M15.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M15/Sample_M15.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M15-Sample_M15.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M18/Sample_M18.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M18/Sample_M18.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M18-Sample_M18.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M2/Sample_M2.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M2/Sample_M2.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M2-Sample_M2.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M20/Sample_M20.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M20/Sample_M20.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M20-Sample_M20.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M23/Sample_M23.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M23/Sample_M23.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M23-Sample_M23.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M24/Sample_M24.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M24/Sample_M24.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M24-Sample_M24.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M26/Sample_M26.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M26/Sample_M26.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M26-Sample_M26.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M27/Sample_M27.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M27/Sample_M27.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M27-Sample_M27.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M28/Sample_M28.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M28/Sample_M28.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M28-Sample_M28.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M29/Sample_M29.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M29/Sample_M29.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M29-Sample_M29.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M3/Sample_M3.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M3/Sample_M3.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M3-Sample_M3.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M31/Sample_M31.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M31/Sample_M31.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M31-Sample_M31.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M32/Sample_M32.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M32/Sample_M32.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M32-Sample_M32.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M33/Sample_M33.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M33/Sample_M33.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M33-Sample_M33.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M34/Sample_M34.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M34/Sample_M34.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M34-Sample_M34.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M35/Sample_M35.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M35/Sample_M35.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M35-Sample_M35.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M4/Sample_M4.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M4/Sample_M4.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M4-Sample_M4.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M40/Sample_M40.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M40/Sample_M40.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M40-Sample_M40.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M42/Sample_M42.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M42/Sample_M42.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M42-Sample_M42.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M43/Sample_M43.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M43/Sample_M43.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M43-Sample_M43.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M46/Sample_M46.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M46/Sample_M46.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M46-Sample_M46.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M48/Sample_M48.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M48/Sample_M48.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M48-Sample_M48.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M5/Sample_M5.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M5/Sample_M5.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M5-Sample_M5.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M9/Sample_M9.forward_paired.fq /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M9/Sample_M9.reverse_paired.fq | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - 150226-Sample_M9-Sample_M9.2x100mers.unique