cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed.mito.fa > P.biaurelia-Sample_379-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.biaurelia-Sample_76-SPAdes-3.5.0-trimmed.mito.fa > P.biaurelia-Sample_76-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed.mito.fa > P.biaurelia-Sample_USBL-36I1-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed.mito.fa > P.caudatum-Sample_C065-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed.mito.fa > P.caudatum-Sample_C083-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed.mito.fa > P.caudatum-Sample_C104-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.caudatum-Sample_C119-SPAdes-3.5.0-trimmed.mito.fa > P.caudatum-Sample_C119-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.caudatum-Sample_C147-SPAdes-3.5.0-trimmed.mito.fa > P.caudatum-Sample_C147-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.multimicronucleatum-Sample_M03-SPAdes-3.5.0-trimmed.mito.fa > P.multimicronucleatum-Sample_M03-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed.mito.fa > P.multimicronucleatum-Sample_M04-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed.mito.fa > P.multimicronucleatum-Sample_M05-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed.mito.fa > P.octaurelia-Sample_1038-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_126-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_127-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_128-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_130-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_131-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_132-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_133-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_134-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_137-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_Indo1-7I-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed.mito.fa > P.sexaurelia-Sample_Moz13BIII-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed.mito.fa > P.tetraurelia-Sample_291-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.tetraurelia-Sample_298-SPAdes-3.5.0-trimmed.mito.fa > P.tetraurelia-Sample_298-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed.mito.fa > P.tetraurelia-Sample_99-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed.mito.fa > P.tetraurelia-Sample_A-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm Sample_C026-SPAdes-3.5.0-trimmed.mito.fa > Sample_C026-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm Sample_Canal-1I-SPAdes-3.5.0-trimmed.mito.fa > Sample_Canal-1I-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm Sample_M08-SPAdes-3.5.0-trimmed.mito.fa > Sample_M08-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm Sample_M13-SPAdes-3.5.0-trimmed.mito.fa > Sample_M13-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm Sample_M15-SPAdes-3.5.0-trimmed.mito.fa > Sample_M15-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan
cd /N/dc2/projects/marinovg/2015-09-07-assemblies/mito; /N/dc2/projects/marinovg/programs/infernal-1.1.1-linux-intel-gcc/binaries/cmscan /N/dc2/projects/marinovg/genomes/Rfam/Rfam12/Rfam.cm Sample_Peniche3I-SPAdes-3.5.0-trimmed.mito.fa > Sample_Peniche3I-SPAdes-3.5.0-trimmed.mito.RFAM12-cmscan