cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_C026-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-Sample_C026-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_C026-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_M13-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-Sample_M13-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_M13-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_Peniche3I-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-Sample_Peniche3I-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_Peniche3I-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/2016-03-17-realignment; python /N/dc2/projects/marinovg/code/SAMstats.py Sample_TRB101-4-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique.bam SAMstats-Sample_TRB101-4-SPAdes-3.5.0-trimmed.realignment.bowtie.PE-v3.unique -bam /N/dc2/projects/marinovg/2015-09-07-assemblies/Sample_TRB101-4-SPAdes-3.5.0-trimmed/scaffolds.chrom.sizes samtools