cd /N/dc2/projects/marinovg/2015-04-22-TFs; module load hmmer/3.0; hmmscan --cpu 16 -o Oxytricha_trifallax_asm_v1.1.ORF.renamed.PFam-27-A --tblout Oxytricha_trifallax_asm_v1.1.ORF.renamed-hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm Oxytricha_trifallax_asm_v1.1.ORF.renamed.fa
cd /N/dc2/projects/marinovg/2015-04-22-TFs; module load hmmer/3.0; hmmscan --cpu 16 -o Paramecium_biaurelia_V1-4.biaurelia_V1-4_annotation_v1.ORF.renamed.PFam-27-A --tblout Paramecium_biaurelia_V1-4.biaurelia_V1-4_annotation_v1.ORF.renamed-hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm Paramecium_biaurelia_V1-4.biaurelia_V1-4_annotation_v1.ORF.renamed.fa
cd /N/dc2/projects/marinovg/2015-04-22-TFs; module load hmmer/3.0; hmmscan --cpu 16 -o Paramecium_caudatum_43c3d.caudatum_43c3d_annotation_v1.ORF.renamed.PFam-27-A --tblout Paramecium_caudatum_43c3d.caudatum_43c3d_annotation_v1.ORF.renamed-hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm Paramecium_caudatum_43c3d.caudatum_43c3d_annotation_v1.ORF.renamed.fa
cd /N/dc2/projects/marinovg/2015-04-22-TFs; module load hmmer/3.0; hmmscan --cpu 16 -o Paramecium_multimicronucleatum_MO3c4.multimicronucleatum_MO3c4_annotation_v1.ORF.renamed.PFam-27-A --tblout Paramecium_multimicronucleatum_MO3c4.multimicronucleatum_MO3c4_annotation_v1.ORF.renamed-hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm Paramecium_multimicronucleatum_MO3c4.multimicronucleatum_MO3c4_annotation_v1.ORF.renamed.fa
cd /N/dc2/projects/marinovg/2015-04-22-TFs; module load hmmer/3.0; hmmscan --cpu 16 -o Paramecium_primaurelia_Ir4-2.primaurelia_Ir4-2_annotation_v1.ORF.renamed.PFam-27-A --tblout Paramecium_primaurelia_Ir4-2.primaurelia_Ir4-2_annotation_v1.ORF.renamed-hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm Paramecium_primaurelia_Ir4-2.primaurelia_Ir4-2_annotation_v1.ORF.renamed.fa
cd /N/dc2/projects/marinovg/2015-04-22-TFs; module load hmmer/3.0; hmmscan --cpu 16 -o Paramecium_sexaurelia_AZ8-4.sexaurelia_AZ8-4_annotation_v1.ORF.renamed.PFam-27-A --tblout Paramecium_sexaurelia_AZ8-4.sexaurelia_AZ8-4_annotation_v1.ORF.renamed-hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm Paramecium_sexaurelia_AZ8-4.sexaurelia_AZ8-4_annotation_v1.ORF.renamed.fa
cd /N/dc2/projects/marinovg/2015-04-22-TFs; module load hmmer/3.0; hmmscan --cpu 16 -o Paramecium_tetraurelia.GCA_000165425.Paramecium_tetraurelia.GCA_000165425.1.20.ORF.renamed.PFam-27-A --tblout Paramecium_tetraurelia.GCA_000165425.Paramecium_tetraurelia.GCA_000165425.1.20.ORF.renamed-hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm Paramecium_tetraurelia.GCA_000165425.Paramecium_tetraurelia.GCA_000165425.1.20.ORF.renamed.fa
cd /N/dc2/projects/marinovg/2015-04-22-TFs; module load hmmer/3.0; hmmscan --cpu 16 -o Stylonychia_lemnae_asm_v1.0_genomic.ORF.renamed.PFam-27-A --tblout Stylonychia_lemnae_asm_v1.0_genomic.ORF.renamed-hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm Stylonychia_lemnae_asm_v1.0_genomic.ORF.renamed.fa
cd /N/dc2/projects/marinovg/2015-04-22-TFs; module load hmmer/3.0; hmmscan --cpu 16 -o Tetrahymena_thermophila.JCVI-TTA1-2.2.20.protein_coding.ORF.renamed.PFam-27-A --tblout Tetrahymena_thermophila.JCVI-TTA1-2.2.20.protein_coding.ORF.renamed-hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm Tetrahymena_thermophila.JCVI-TTA1-2.2.20.protein_coding.ORF.renamed.fa