cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/TAIR10/Arabidopsis_thaliana.TAIR10.19.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/TAIR10/Arabidopsis_thaliana.TAIR10.19.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/TAIR10/Arabidopsis_thaliana.TAIR10.19.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Aegilops_tauschii/Aegilops_tauschii.GCA_000347335.1.19.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Aegilops_tauschii/Aegilops_tauschii.GCA_000347335.1.19.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Aegilops_tauschii/Aegilops_tauschii.GCA_000347335.1.19.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Glycine_max/Glycine_max.V1.0.19.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Glycine_max/Glycine_max.V1.0.19.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Glycine_max/Glycine_max.V1.0.19.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Hordeum_vulgare/Hordeum_vulgare.030312v2.19.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Hordeum_vulgare/Hordeum_vulgare.030312v2.19.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Hordeum_vulgare/Hordeum_vulgare.030312v2.19.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.19.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.19.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.19.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Populus_trichocarpa/Populus_trichocarpa.JGI2.0.19.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Populus_trichocarpa/Populus_trichocarpa.JGI2.0.19.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Populus_trichocarpa/Populus_trichocarpa.JGI2.0.19.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Selaginella_moellendorffii/Selaginella_moellendorffii.v1.0.19.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Selaginella_moellendorffii/Selaginella_moellendorffii.v1.0.19.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Selaginella_moellendorffii/Selaginella_moellendorffii.v1.0.19.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Setaria_italica/Setaria_italica.JGIv2.0.19.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Setaria_italica/Setaria_italica.JGIv2.0.19.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Setaria_italica/Setaria_italica.JGIv2.0.19.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Sorghum_bicolor/Sorghum_bicolor.Sorbi1.19.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Sorghum_bicolor/Sorghum_bicolor.Sorbi1.19.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Sorghum_bicolor/Sorghum_bicolor.Sorbi1.19.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Triticum_urartu/Triticum_urartu.GCA_000347455.1.19.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Triticum_urartu/Triticum_urartu.GCA_000347455.1.19.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Triticum_urartu/Triticum_urartu.GCA_000347455.1.19.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Vitis_vinifera/Vitis_vinifera.IGGP_12x.19.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Vitis_vinifera/Vitis_vinifera.IGGP_12x.19.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Vitis_vinifera/Vitis_vinifera.IGGP_12x.19.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-25-PRC; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.19.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.19.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.19.fixed.ORF.fa