cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Babesia_bovis-ASM16539v1/GCA_000165395.1_ASM16539v1_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Babesia_bovis-ASM16539v1/GCA_000165395.1_ASM16539v1_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Babesia_bovis-ASM16539v1/GCA_000165395.1_ASM16539v1_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Babesia_equi-strainWA-JCVI-bewag-v1.1/GCA_000342415.1_JCVI-bewag-v1.1_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Babesia_equi-strainWA-JCVI-bewag-v1.1/GCA_000342415.1_JCVI-bewag-v1.1_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Babesia_equi-strainWA-JCVI-bewag-v1.1/GCA_000342415.1_JCVI-bewag-v1.1_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Babesia_microti-strainRI-ASM69194v1/GCA_000691945.1_ASM69194v1_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Babesia_microti-strainRI-ASM69194v1/GCA_000691945.1_ASM69194v1_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Babesia_microti-strainRI-ASM69194v1/GCA_000691945.1_ASM69194v1_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Cryptosporidium_hominis-ASM642v1/GCF_000006425.1_ASM642v1_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Cryptosporidium_hominis-ASM642v1/GCF_000006425.1_ASM642v1_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Cryptosporidium_hominis-ASM642v1/GCF_000006425.1_ASM642v1_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Cryptosporidium_muris-RN66-JCVI-cmg-v1.0/GCA_000006515.1_JCVI_cmg_v1.0_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Cryptosporidium_muris-RN66-JCVI-cmg-v1.0/GCA_000006515.1_JCVI_cmg_v1.0_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Cryptosporidium_muris-RN66-JCVI-cmg-v1.0/GCA_000006515.1_JCVI_cmg_v1.0_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Cryptosporidium_parvum-IowaII-ASM16534v1/GCA_000165345.1_ASM16534v1_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Cryptosporidium_parvum-IowaII-ASM16534v1/GCA_000165345.1_ASM16534v1_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Cryptosporidium_parvum-IowaII-ASM16534v1/GCA_000165345.1_ASM16534v1_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_acervulina-EAH001/GCA_000499425.1_EAH001_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_acervulina-EAH001/GCA_000499425.1_EAH001_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_acervulina-EAH001/GCA_000499425.1_EAH001_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_brunetti-EBH001/GCA_000499725.1_EBH001_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_brunetti-EBH001/GCA_000499725.1_EBH001_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_brunetti-EBH001/GCA_000499725.1_EBH001_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_maxima-EMW001/GCA_000499605.1_EMW001_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_maxima-EMW001/GCA_000499605.1_EMW001_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_maxima-EMW001/GCA_000499605.1_EMW001_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_mitis-EMH001/GCA_000499745.1_EMH001_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_mitis-EMH001/GCA_000499745.1_EMH001_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_mitis-EMH001/GCA_000499745.1_EMH001_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_necatrix-ENH001/GCA_000499385.1_ENH001_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_necatrix-ENH001/GCA_000499385.1_ENH001_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_necatrix-ENH001/GCA_000499385.1_ENH001_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_praecox-EPH001/GCA_000499445.1_EPH001_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_praecox-EPH001/GCA_000499445.1_EPH001_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria_praecox-EPH001/GCA_000499445.1_EPH001_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria-tenella-ETH001/GCA_000499545.1_ETH001_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria-tenella-ETH001/GCA_000499545.1_ETH001_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Eimeria-tenella-ETH001/GCA_000499545.1_ETH001_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Gregarina_niphandrodes-GNI3/GCA_000223845.4_GNI3_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Gregarina_niphandrodes-GNI3/GCA_000223845.4_GNI3_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Gregarina_niphandrodes-GNI3/GCA_000223845.4_GNI3_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Hammondia_hammondi-HHA1v02/GCA_000258005.2_HHA1_v02_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Hammondia_hammondi-HHA1v02/GCA_000258005.2_HHA1_v02_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Hammondia_hammondi-HHA1v02/GCA_000258005.2_HHA1_v02_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Neospora_caninum-Liverpool-ASM20886v2/GCA_000208865.2_ASM20886v2_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Neospora_caninum-Liverpool-ASM20886v2/GCA_000208865.2_ASM20886v2_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Neospora_caninum-Liverpool-ASM20886v2/GCA_000208865.2_ASM20886v2_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Theileria_orientalis-strain-Shintoku-ASM74089v1/GCA_000740895.1_ASM74089v1_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Theileria_orientalis-strain-Shintoku-ASM74089v1/GCA_000740895.1_ASM74089v1_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Theileria_orientalis-strain-Shintoku-ASM74089v1/GCA_000740895.1_ASM74089v1_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Theileria_parva-ASM16536v1/GCA_000165365.1_ASM16536v1_protein.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Theileria_parva-ASM16536v1/GCA_000165365.1_ASM16536v1_protein.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Theileria_parva-ASM16536v1/GCA_000165365.1_ASM16536v1_protein.faa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_berghei/Plasmodium_berghei.May_2010.20.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_berghei/Plasmodium_berghei.May_2010.20.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_berghei/Plasmodium_berghei.May_2010.20.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_chabaudi/Plasmodium_chabaudi.May_2010.20.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_chabaudi/Plasmodium_chabaudi.May_2010.20.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_chabaudi/Plasmodium_chabaudi.May_2010.20.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_knowlesi/Plasmodium_knowlesi.EPr1.20.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_knowlesi/Plasmodium_knowlesi.EPr1.20.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_knowlesi/Plasmodium_knowlesi.EPr1.20.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_vivax/Plasmodium_vivax.ASM241v1.20.fixed.ORF.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_vivax/Plasmodium_vivax.ASM241v1.20.fixed.ORF.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_vivax/Plasmodium_vivax.ASM241v1.20.fixed.ORF.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_berghei/sequence/Plasmodium_berghei.May_2010.20.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_berghei/sequence/Plasmodium_berghei.May_2010.20.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_berghei/sequence/Plasmodium_berghei.May_2010.20.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_chabaudi/sequence/Plasmodium_chabaudi.May_2010.20.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_chabaudi/sequence/Plasmodium_chabaudi.May_2010.20.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_chabaudi/sequence/Plasmodium_chabaudi.May_2010.20.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_knowlesi/sequence/Plasmodium_knowlesi.EPr1.20.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_knowlesi/sequence/Plasmodium_knowlesi.EPr1.20.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_knowlesi/sequence/Plasmodium_knowlesi.EPr1.20.fa
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-08-13-DNMTs; module load hmmer/3.0; hmmscan --cpu 16 -o /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_vivax/sequence/Plasmodium_vivax.ASM241v1.20.PFam-27-A --tblout /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_vivax/sequence/Plasmodium_vivax.ASM241v1.20.hmmscan.tblout /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm /N/dc2/projects/marinovg/genomes/Apicomplexa/Plasmodium_vivax/sequence/Plasmodium_vivax.ASM241v1.20.fa