###################################################################### MFANNOT, ORGANELLAR GENOME ANNOTATION PROGRAM VERSION 1.35 Programmed by N. Beck and P. Rioux ###################################################################### ---------------------------------- General Options ---------------------------------- Masterfile used : hcw2_mt_scaffolded.fasta New Masterfile created : /working-dir/hcw2_mt_scaffolded.fasta.new Genetic code : 4 Logfile : logfile_hcw2.txt Usage of RNAweasel The Path of configfile is : /MFannot_data/config/.mfannot_external_programs.conf The Path of pattern file is : /MFannot_data/config/.motsearch.pat Look in the peptide library /MFannot_data/protein_collections//identified ---------------------------------- Gene Annotation ---------------------------------- Options : Minimum size ORF, for flip running 40 Blast e-value cutoff : 1e-10 Minimum exon size : 3 Maximum intron size : 4000 Minimum intron size : 142 Matrix : BLOSUM62 Minimum length of non corresponding ORFs : 300 Overlapping cutoff for non-corresponding ORFs: 30 Parsing masterfile hcw2_mt_scaffolded.fasta... Number of contigs in Masterfile : 3 Number of annotations (or comments) detected : 0 1) Translate (flip)... Making local copy of masterfile with no CRs. /usr/local/bin/flip -m -l 40 -g 4 mf_noCr.all > /working-dir/tmp_hcw2/flip.output 2) Blast... /usr/bin/makeblastdb -in /working-dir/tmp_hcw2/library.pep -dbtype prot -out /working-dir/tmp_hcw2/mf >/dev/null 2>/dev/null nice -19 /usr/bin/blastp -outfmt 5 -matrix BLOSUM62 -db /working-dir/tmp_hcw2/mf -query /working-dir/tmp_hcw2/prot.lst -out /working-dir/tmp_hcw2/blastoutput.xml 2> /working-dir/tmp_hcw2/blasterr_1.txt 3) Parse Blast Results... 4) Select best proteins for Exonerate... 5) Annotate genes w/o introns... /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/nad62ddf5c8/nad6.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/nad62ddf5c8/nad6.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/nad62ddf5c8/nad6.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/nad62ddf5c8/nad6.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/nad62ddf5c8/nad6.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad62ddf5c8/nad6.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/nad62ddf5c8/nad6.aln /working-dir/tmp_hcw2/HMM_For_Start/nad62ddf5c8/nad6.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad62ddf5c8/nad6.seq >/dev/null 2>/dev/null /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/nad32d3f580/nad3.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/nad32d3f580/nad3.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/nad32d3f580/nad3.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/nad32d3f580/nad3.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/nad32d3f580/nad3.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad32d3f580/nad3.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/nad32d3f580/nad3.aln /working-dir/tmp_hcw2/HMM_For_Start/nad32d3f580/nad3.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad32d3f580/nad3.seq >/dev/null 2>/dev/null /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/nad4L2d3d788/nad4L.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/nad4L2d3d788/nad4L.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/nad4L2d3d788/nad4L.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/nad4L2d3d788/nad4L.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/nad4L2d3d788/nad4L.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad4L2d3d788/nad4L.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/nad4L2d3d788/nad4L.aln /working-dir/tmp_hcw2/HMM_For_Start/nad4L2d3d788/nad4L.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad4L2d3d788/nad4L.seq >/dev/null 2>/dev/null 6) Intron identification... DEBUG: Executing external script block 'B-0' for 'IntronI'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronI.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.IntronI.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.IntronI.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronI.B-0.MfGC.1 START --- # Setup work dir. mkdir /working-dir/tmp_hcw2/intronI cd /working-dir/tmp_hcw2/intronI RNAfinder -m IntronI -g 4 -d /working-dir/tmp_hcw2/Contig/contig2 -M /working-dir/tmp_hcw2/Contig/contig2-IntronI.xml # cd ..;rm -rf intronI --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronI.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'IntronI'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronI.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.IntronI.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.IntronI.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronI.B-0.MfGC.1 START --- # Setup work dir. mkdir /working-dir/tmp_hcw2/intronI cd /working-dir/tmp_hcw2/intronI RNAfinder -m IntronI -g 4 -d /working-dir/tmp_hcw2/Contig/contig3 -M /working-dir/tmp_hcw2/Contig/contig3-IntronI.xml # cd ..;rm -rf intronI --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronI.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'IntronI'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronI.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.IntronI.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.IntronI.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronI.B-0.MfGC.1 START --- # Setup work dir. mkdir /working-dir/tmp_hcw2/intronI cd /working-dir/tmp_hcw2/intronI RNAfinder -m IntronI -g 4 -d /working-dir/tmp_hcw2/Contig/contig1 -M /working-dir/tmp_hcw2/Contig/contig1-IntronI.xml # cd ..;rm -rf intronI --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronI.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'IntronII'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronII.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.IntronII.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.IntronII.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronII.B-0.MfGC.1 START --- # Setup work dir. mkdir /working-dir/tmp_hcw2/intronII cd /working-dir/tmp_hcw2/intronII RNAfinder -m IntronII -g 4 -d /working-dir/tmp_hcw2/Contig/contig2 -M /working-dir/tmp_hcw2/Contig/contig2-IntronII.xml # cd ..;rm -rf intronII --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronII.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'IntronII'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronII.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.IntronII.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.IntronII.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronII.B-0.MfGC.1 START --- # Setup work dir. mkdir /working-dir/tmp_hcw2/intronII cd /working-dir/tmp_hcw2/intronII RNAfinder -m IntronII -g 4 -d /working-dir/tmp_hcw2/Contig/contig3 -M /working-dir/tmp_hcw2/Contig/contig3-IntronII.xml # cd ..;rm -rf intronII --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronII.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'IntronII'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronII.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.IntronII.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.IntronII.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronII.B-0.MfGC.1 START --- # Setup work dir. mkdir /working-dir/tmp_hcw2/intronII cd /working-dir/tmp_hcw2/intronII RNAfinder -m IntronII -g 4 -d /working-dir/tmp_hcw2/Contig/contig1 -M /working-dir/tmp_hcw2/Contig/contig1-IntronII.xml # cd ..;rm -rf intronII --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.IntronII.B-0.MfGC.1 END --- 7) Annotate genes with introns... /usr/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /MFannot_data/models/Splice/neutral.pssm --splice5 /MFannot_data/models/Splice/neutral.pssm --geneticcode 4 /working-dir/tmp_hcw2/Exonerate/prot_for_exonerate_0_cox1 '/working-dir/tmp_hcw2/Exonerate/gene_for_exonerate_contig1' > /working-dir/tmp_hcw2/Exonerate/exonerate_0_cox1 /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/cox12d680f8/cox1.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/cox12d680f8/cox1.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/cox12d680f8/cox1.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/cox12d680f8/cox1.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/cox12d680f8/cox1.hmm /working-dir/tmp_hcw2/HMM_For_Start/cox12d680f8/cox1.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/cox12d680f8/cox1.aln /working-dir/tmp_hcw2/HMM_For_Start/cox12d680f8/cox1.hmm /working-dir/tmp_hcw2/HMM_For_Start/cox12d680f8/cox1.seq >/dev/null 2>/dev/null /usr/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /MFannot_data/models/Splice/neutral.pssm --splice5 /MFannot_data/models/Splice/neutral.pssm --geneticcode 4 /working-dir/tmp_hcw2/Exonerate/prot_for_exonerate_1_cox2 '/working-dir/tmp_hcw2/Exonerate/gene_for_exonerate_contig1' > /working-dir/tmp_hcw2/Exonerate/exonerate_1_cox2 /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/cox22d7f828/cox2.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/cox22d7f828/cox2.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/cox22d7f828/cox2.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/cox22d7f828/cox2.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/cox22d7f828/cox2.hmm /working-dir/tmp_hcw2/HMM_For_Start/cox22d7f828/cox2.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/cox22d7f828/cox2.aln /working-dir/tmp_hcw2/HMM_For_Start/cox22d7f828/cox2.hmm /working-dir/tmp_hcw2/HMM_For_Start/cox22d7f828/cox2.seq >/dev/null 2>/dev/null /usr/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /MFannot_data/models/Splice/neutral.pssm --splice5 /MFannot_data/models/Splice/neutral.pssm --geneticcode 4 /working-dir/tmp_hcw2/Exonerate/prot_for_exonerate_2_nad4 '/working-dir/tmp_hcw2/Exonerate/gene_for_exonerate_contig1' > /working-dir/tmp_hcw2/Exonerate/exonerate_2_nad4 /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/nad42dbaa48/nad4.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/nad42dbaa48/nad4.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/nad42dbaa48/nad4.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/nad42dbaa48/nad4.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/nad42dbaa48/nad4.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad42dbaa48/nad4.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/nad42dbaa48/nad4.aln /working-dir/tmp_hcw2/HMM_For_Start/nad42dbaa48/nad4.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad42dbaa48/nad4.seq >/dev/null 2>/dev/null /usr/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /MFannot_data/models/Splice/neutral.pssm --splice5 /MFannot_data/models/Splice/neutral.pssm --geneticcode 4 /working-dir/tmp_hcw2/Exonerate/prot_for_exonerate_3_nad1 '/working-dir/tmp_hcw2/Exonerate/gene_for_exonerate_contig1' > /working-dir/tmp_hcw2/Exonerate/exonerate_3_nad1 /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/nad12dc00b8/nad1.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/nad12dc00b8/nad1.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/nad12dc00b8/nad1.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/nad12dc00b8/nad1.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/nad12dc00b8/nad1.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad12dc00b8/nad1.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/nad12dc00b8/nad1.aln /working-dir/tmp_hcw2/HMM_For_Start/nad12dc00b8/nad1.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad12dc00b8/nad1.seq >/dev/null 2>/dev/null /usr/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /MFannot_data/models/Splice/neutral.pssm --splice5 /MFannot_data/models/Splice/neutral.pssm --geneticcode 4 /working-dir/tmp_hcw2/Exonerate/prot_for_exonerate_4_cob '/working-dir/tmp_hcw2/Exonerate/gene_for_exonerate_contig1' > /working-dir/tmp_hcw2/Exonerate/exonerate_4_cob /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/cob2d68350/cob.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/cob2d68350/cob.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/cob2d68350/cob.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/cob2d68350/cob.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/cob2d68350/cob.hmm /working-dir/tmp_hcw2/HMM_For_Start/cob2d68350/cob.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/cob2d68350/cob.aln /working-dir/tmp_hcw2/HMM_For_Start/cob2d68350/cob.hmm /working-dir/tmp_hcw2/HMM_For_Start/cob2d68350/cob.seq >/dev/null 2>/dev/null /usr/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /MFannot_data/models/Splice/neutral.pssm --splice5 /MFannot_data/models/Splice/neutral.pssm --geneticcode 4 /working-dir/tmp_hcw2/Exonerate/prot_for_exonerate_5_atp6 '/working-dir/tmp_hcw2/Exonerate/gene_for_exonerate_contig1' > /working-dir/tmp_hcw2/Exonerate/exonerate_5_atp6 /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/atp62e04af8/atp6.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/atp62e04af8/atp6.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/atp62e04af8/atp6.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/atp62e04af8/atp6.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/atp62e04af8/atp6.hmm /working-dir/tmp_hcw2/HMM_For_Start/atp62e04af8/atp6.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/atp62e04af8/atp6.aln /working-dir/tmp_hcw2/HMM_For_Start/atp62e04af8/atp6.hmm /working-dir/tmp_hcw2/HMM_For_Start/atp62e04af8/atp6.seq >/dev/null 2>/dev/null /usr/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /MFannot_data/models/Splice/neutral.pssm --splice5 /MFannot_data/models/Splice/neutral.pssm --geneticcode 4 /working-dir/tmp_hcw2/Exonerate/prot_for_exonerate_6_cox3 '/working-dir/tmp_hcw2/Exonerate/gene_for_exonerate_contig1' > /working-dir/tmp_hcw2/Exonerate/exonerate_6_cox3 /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/cox32d651c0/cox3.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/cox32d651c0/cox3.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/cox32d651c0/cox3.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/cox32d651c0/cox3.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/cox32d651c0/cox3.hmm /working-dir/tmp_hcw2/HMM_For_Start/cox32d651c0/cox3.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/cox32d651c0/cox3.aln /working-dir/tmp_hcw2/HMM_For_Start/cox32d651c0/cox3.hmm /working-dir/tmp_hcw2/HMM_For_Start/cox32d651c0/cox3.seq >/dev/null 2>/dev/null /usr/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /MFannot_data/models/Splice/neutral.pssm --splice5 /MFannot_data/models/Splice/neutral.pssm --geneticcode 4 /working-dir/tmp_hcw2/Exonerate/prot_for_exonerate_7_nad2 '/working-dir/tmp_hcw2/Exonerate/gene_for_exonerate_contig1' > /working-dir/tmp_hcw2/Exonerate/exonerate_7_nad2 /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/nad22d4cdd0/nad2.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/nad22d4cdd0/nad2.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/nad22d4cdd0/nad2.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/nad22d4cdd0/nad2.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/nad22d4cdd0/nad2.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad22d4cdd0/nad2.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/nad22d4cdd0/nad2.aln /working-dir/tmp_hcw2/HMM_For_Start/nad22d4cdd0/nad2.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad22d4cdd0/nad2.seq >/dev/null 2>/dev/null /usr/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /MFannot_data/models/Splice/neutral.pssm --splice5 /MFannot_data/models/Splice/neutral.pssm --geneticcode 4 /working-dir/tmp_hcw2/Exonerate/prot_for_exonerate_8_nad5 '/working-dir/tmp_hcw2/Exonerate/gene_for_exonerate_contig1' > /working-dir/tmp_hcw2/Exonerate/exonerate_8_nad5 /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Start/nad52ded000/nad5.homo' -out '/working-dir/tmp_hcw2/HMM_For_Start/nad52ded000/nad5.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Start/nad52ded000/nad5.pir' -o '/working-dir/tmp_hcw2/HMM_For_Start/nad52ded000/nad5.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Start/nad52ded000/nad5.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad52ded000/nad5.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Start/nad52ded000/nad5.aln /working-dir/tmp_hcw2/HMM_For_Start/nad52ded000/nad5.hmm /working-dir/tmp_hcw2/HMM_For_Start/nad52ded000/nad5.seq >/dev/null 2>/dev/null 8) Identify gene fusions... 9) Annotate mini exons... /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.aln /working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cox1_2d680f8/cox1_0.ali' -f clustal >/dev/null 2>/dev/null /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.aln /working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cox2_2d7f828/cox2_0.ali' -f clustal >/dev/null 2>/dev/null /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.aln /working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/nad4_2dbaa48/nad4_0.ali' -f clustal >/dev/null 2>/dev/null /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.aln /working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/nad1_2dc00b8/nad1_0.ali' -f clustal >/dev/null 2>/dev/null /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.aln /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_0.ali' -f clustal >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/i4_0.fas' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/i4_0.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/i4_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/i4_0.ali >/dev/null 2>/dev/null nice -19 /usr/bin/hmmsearch -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/i4_0_z0.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/i4_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/i4_0_z0.fas /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_0' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_0.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_0.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_0_1' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_0_1.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_0_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_0_1.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_1' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_1.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_1.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_1_1' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_1_1.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_1_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_1_1.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_2' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_2.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_2.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_2.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_2_1' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_2_1.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_2_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_2_1.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_3' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_3.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_3.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_3.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_3_1' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_3_1.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_3_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_3_1.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_4' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_4.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_4.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_4.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_4_1' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_4_1.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_4_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_4_1.ali >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_3_1' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_3_1.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_3_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_3_1.ali >/dev/null 2>/dev/null nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_1.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_1.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_3.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_3.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_3.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_2_1.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_2_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_2_1.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_3_1.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_3_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_3_1.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_3_1.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_3_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_3_1.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_4_1.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_4_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_4_1.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_4.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_4.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_4.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_1_1.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_1_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_1_1.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_0.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_0.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_0_1.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_0_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_4_0_1.fas nice -19 /usr/bin/hmmsearch --noali --max -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_2.res /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_2.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/intron4_it0_5_2.fas /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.aln /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cob_2d68350/cob_1.ali' -f clustal >/dev/null 2>/dev/null /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.aln /working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/atp6_2e04af8/atp6_0.ali' -f clustal >/dev/null 2>/dev/null /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.aln /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/cox3_0.ali' -f clustal >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0.fas' -o '/working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0.ali' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild --amino /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0.ali >/dev/null 2>/dev/null nice -19 /usr/bin/hmmsearch -o /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0_z0.res /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0_z0.fas nice -19 /usr/bin/hmmsearch -o /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0_z1.res /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/cox3_2d651c0/i2_0_z1.fas /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.aln /working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/nad2_2d4cdd0/nad2_0.ali' -f clustal >/dev/null 2>/dev/null /usr/local/bin/muscle -in '/working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.homo' -out '/working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.pir' >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.pir' -o '/working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /usr/bin/hmmbuild /working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.sto >/dev/null 2>/dev/null nice -19 /usr/bin/hmmalign --trim --outformat stockholm -o /working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.aln /working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.hmm /working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.seq >/dev/null 2>/dev/null /usr/local/bin/umac -i '/working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.aln' -o '/working-dir/tmp_hcw2/HMM_For_Exo/nad5_2ded000/nad5_0.ali' -f clustal >/dev/null 2>/dev/null 10) Annotate RNA genes... DEBUG: Executing external script block 'B-0' for 'rns'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rns.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rns.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rns.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rns.B-0.MfGC.1 START --- mkdir /working-dir/tmp_hcw2/RNS HMMsearchWrapper -c "start of 5'" -o /working-dir/tmp_hcw2/RNS/5-rns-fungi.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/5-rns-fungi.hmm -n rns HMMsearchWrapper -c "start of 5'" -o /working-dir/tmp_hcw2/RNS/5-rns-other.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/5-rns-other.hmm -n rns HMMsearchWrapper -c "end of 3'" -o /working-dir/tmp_hcw2/RNS/3-rns-fungi.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/3-rns-fungi.hmm -n rns HMMsearchWrapper -c "end of 3'" -o /working-dir/tmp_hcw2/RNS/3-rns-other.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/3-rns-other.hmm -n rns HMMsearchWrapper -c "corr to pos 89-113 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_89-113.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/rns_89-113.hmm -n rns HMMsearchWrapper -c "corr to pos 358-392 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_358-392.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/rns_358-392.hmm -n rns HMMsearchWrapper -c "corr to pos 485-571 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_485-571.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/rns_485-571.hmm -n rns HMMsearchWrapper -c "corr to pos 735-810 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_735-810.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/rns_735-810.hmm -n rns HMMsearchWrapper -c "corr to pos 850-965 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_850-965.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/rns_850-965.hmm -n rns HMMsearchWrapper -c "corr to pos 1014-1044 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_1014-1044.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/rns_1014-1044.hmm -n rns HMMsearchWrapper -c "corr to pos 1190-1252 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_1190-1252.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/rns_1190-1252.hmm -n rns HMMsearchWrapper -c "corr to pos 1305-1411 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_1305-1411.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/rns_1305-1411.hmm -n rns HMMsearchCombiner -o /working-dir/tmp_hcw2/Contig/contig2-rns.xml \ /working-dir/tmp_hcw2/RNS/5-rns-fungi.xml \ /working-dir/tmp_hcw2/RNS/5-rns-other.xml \ /working-dir/tmp_hcw2/RNS/3-rns-fungi.xml \ /working-dir/tmp_hcw2/RNS/3-rns-other.xml \ /working-dir/tmp_hcw2/RNS/rns_89-113.xml \ /working-dir/tmp_hcw2/RNS/rns_358-392.xml \ /working-dir/tmp_hcw2/RNS/rns_485-571.xml \ /working-dir/tmp_hcw2/RNS/rns_735-810.xml \ /working-dir/tmp_hcw2/RNS/rns_850-965.xml \ /working-dir/tmp_hcw2/RNS/rns_1014-1044.xml \ /working-dir/tmp_hcw2/RNS/rns_1190-1252.xml \ /working-dir/tmp_hcw2/RNS/rns_1305-1411.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rns.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rns'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rns.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rns.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rns.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rns.B-0.MfGC.1 START --- mkdir /working-dir/tmp_hcw2/RNS HMMsearchWrapper -c "start of 5'" -o /working-dir/tmp_hcw2/RNS/5-rns-fungi.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/5-rns-fungi.hmm -n rns HMMsearchWrapper -c "start of 5'" -o /working-dir/tmp_hcw2/RNS/5-rns-other.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/5-rns-other.hmm -n rns HMMsearchWrapper -c "end of 3'" -o /working-dir/tmp_hcw2/RNS/3-rns-fungi.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/3-rns-fungi.hmm -n rns HMMsearchWrapper -c "end of 3'" -o /working-dir/tmp_hcw2/RNS/3-rns-other.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/3-rns-other.hmm -n rns HMMsearchWrapper -c "corr to pos 89-113 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_89-113.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/rns_89-113.hmm -n rns HMMsearchWrapper -c "corr to pos 358-392 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_358-392.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/rns_358-392.hmm -n rns HMMsearchWrapper -c "corr to pos 485-571 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_485-571.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/rns_485-571.hmm -n rns HMMsearchWrapper -c "corr to pos 735-810 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_735-810.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/rns_735-810.hmm -n rns HMMsearchWrapper -c "corr to pos 850-965 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_850-965.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/rns_850-965.hmm -n rns HMMsearchWrapper -c "corr to pos 1014-1044 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_1014-1044.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/rns_1014-1044.hmm -n rns HMMsearchWrapper -c "corr to pos 1190-1252 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_1190-1252.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/rns_1190-1252.hmm -n rns HMMsearchWrapper -c "corr to pos 1305-1411 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_1305-1411.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/rns_1305-1411.hmm -n rns HMMsearchCombiner -o /working-dir/tmp_hcw2/Contig/contig3-rns.xml \ /working-dir/tmp_hcw2/RNS/5-rns-fungi.xml \ /working-dir/tmp_hcw2/RNS/5-rns-other.xml \ /working-dir/tmp_hcw2/RNS/3-rns-fungi.xml \ /working-dir/tmp_hcw2/RNS/3-rns-other.xml \ /working-dir/tmp_hcw2/RNS/rns_89-113.xml \ /working-dir/tmp_hcw2/RNS/rns_358-392.xml \ /working-dir/tmp_hcw2/RNS/rns_485-571.xml \ /working-dir/tmp_hcw2/RNS/rns_735-810.xml \ /working-dir/tmp_hcw2/RNS/rns_850-965.xml \ /working-dir/tmp_hcw2/RNS/rns_1014-1044.xml \ /working-dir/tmp_hcw2/RNS/rns_1190-1252.xml \ /working-dir/tmp_hcw2/RNS/rns_1305-1411.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rns.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rns'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rns.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rns.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rns.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rns.B-0.MfGC.1 START --- mkdir /working-dir/tmp_hcw2/RNS HMMsearchWrapper -c "start of 5'" -o /working-dir/tmp_hcw2/RNS/5-rns-fungi.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/5-rns-fungi.hmm -n rns HMMsearchWrapper -c "start of 5'" -o /working-dir/tmp_hcw2/RNS/5-rns-other.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/5-rns-other.hmm -n rns HMMsearchWrapper -c "end of 3'" -o /working-dir/tmp_hcw2/RNS/3-rns-fungi.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/3-rns-fungi.hmm -n rns HMMsearchWrapper -c "end of 3'" -o /working-dir/tmp_hcw2/RNS/3-rns-other.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/3-rns-other.hmm -n rns HMMsearchWrapper -c "corr to pos 89-113 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_89-113.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/rns_89-113.hmm -n rns HMMsearchWrapper -c "corr to pos 358-392 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_358-392.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/rns_358-392.hmm -n rns HMMsearchWrapper -c "corr to pos 485-571 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_485-571.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/rns_485-571.hmm -n rns HMMsearchWrapper -c "corr to pos 735-810 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_735-810.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/rns_735-810.hmm -n rns HMMsearchWrapper -c "corr to pos 850-965 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_850-965.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/rns_850-965.hmm -n rns HMMsearchWrapper -c "corr to pos 1014-1044 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_1014-1044.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/rns_1014-1044.hmm -n rns HMMsearchWrapper -c "corr to pos 1190-1252 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_1190-1252.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/rns_1190-1252.hmm -n rns HMMsearchWrapper -c "corr to pos 1305-1411 of R.americana" -e 1 -o /working-dir/tmp_hcw2/RNS/rns_1305-1411.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/rns_1305-1411.hmm -n rns HMMsearchCombiner -o /working-dir/tmp_hcw2/Contig/contig1-rns.xml \ /working-dir/tmp_hcw2/RNS/5-rns-fungi.xml \ /working-dir/tmp_hcw2/RNS/5-rns-other.xml \ /working-dir/tmp_hcw2/RNS/3-rns-fungi.xml \ /working-dir/tmp_hcw2/RNS/3-rns-other.xml \ /working-dir/tmp_hcw2/RNS/rns_89-113.xml \ /working-dir/tmp_hcw2/RNS/rns_358-392.xml \ /working-dir/tmp_hcw2/RNS/rns_485-571.xml \ /working-dir/tmp_hcw2/RNS/rns_735-810.xml \ /working-dir/tmp_hcw2/RNS/rns_850-965.xml \ /working-dir/tmp_hcw2/RNS/rns_1014-1044.xml \ /working-dir/tmp_hcw2/RNS/rns_1190-1252.xml \ /working-dir/tmp_hcw2/RNS/rns_1305-1411.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rns.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rnl'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rnl.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rnl.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rnl.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnl.B-0.MfGC.1 START --- mkdir /working-dir/tmp_hcw2/RNL HMMsearchWrapper -c "5' +/- 50 nt" -l 170 -o /working-dir/tmp_hcw2/RNL/5-rnl-yeast.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/5-rnl-yeast.hmm -n rnl HMMsearchWrapper -c "5' +/- 50 nt" -l 170 -o /working-dir/tmp_hcw2/RNL/5-rnl-other.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/5-rnl-other.hmm -n rnl HMMsearchWrapper -c "3' -20/+180" -r 120 -o /working-dir/tmp_hcw2/RNL/3-rnl-yeast.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/3-rnl-yeast.hmm -n rnl HMMsearchWrapper -c "3' -20/+180" -r 120 -o /working-dir/tmp_hcw2/RNL/3-rnl-other.xml -g /working-dir/tmp_hcw2/Contig/contig2 -m /MFannot_data/models/HMM_models/RNA/3-rnl-other.hmm -n rnl HMMsearchCombiner -o /working-dir/tmp_hcw2/Contig/contig2-rnl.xml \ /working-dir/tmp_hcw2/RNL/5-rnl-yeast.xml \ /working-dir/tmp_hcw2/RNL/5-rnl-other.xml \ /working-dir/tmp_hcw2/RNL/3-rnl-yeast.xml \ /working-dir/tmp_hcw2/RNL/3-rnl-other.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnl.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rnl'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rnl.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rnl.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rnl.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnl.B-0.MfGC.1 START --- mkdir /working-dir/tmp_hcw2/RNL HMMsearchWrapper -c "5' +/- 50 nt" -l 170 -o /working-dir/tmp_hcw2/RNL/5-rnl-yeast.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/5-rnl-yeast.hmm -n rnl HMMsearchWrapper -c "5' +/- 50 nt" -l 170 -o /working-dir/tmp_hcw2/RNL/5-rnl-other.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/5-rnl-other.hmm -n rnl HMMsearchWrapper -c "3' -20/+180" -r 120 -o /working-dir/tmp_hcw2/RNL/3-rnl-yeast.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/3-rnl-yeast.hmm -n rnl HMMsearchWrapper -c "3' -20/+180" -r 120 -o /working-dir/tmp_hcw2/RNL/3-rnl-other.xml -g /working-dir/tmp_hcw2/Contig/contig3 -m /MFannot_data/models/HMM_models/RNA/3-rnl-other.hmm -n rnl HMMsearchCombiner -o /working-dir/tmp_hcw2/Contig/contig3-rnl.xml \ /working-dir/tmp_hcw2/RNL/5-rnl-yeast.xml \ /working-dir/tmp_hcw2/RNL/5-rnl-other.xml \ /working-dir/tmp_hcw2/RNL/3-rnl-yeast.xml \ /working-dir/tmp_hcw2/RNL/3-rnl-other.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnl.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rnl'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rnl.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rnl.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rnl.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnl.B-0.MfGC.1 START --- mkdir /working-dir/tmp_hcw2/RNL HMMsearchWrapper -c "5' +/- 50 nt" -l 170 -o /working-dir/tmp_hcw2/RNL/5-rnl-yeast.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/5-rnl-yeast.hmm -n rnl HMMsearchWrapper -c "5' +/- 50 nt" -l 170 -o /working-dir/tmp_hcw2/RNL/5-rnl-other.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/5-rnl-other.hmm -n rnl HMMsearchWrapper -c "3' -20/+180" -r 120 -o /working-dir/tmp_hcw2/RNL/3-rnl-yeast.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/3-rnl-yeast.hmm -n rnl HMMsearchWrapper -c "3' -20/+180" -r 120 -o /working-dir/tmp_hcw2/RNL/3-rnl-other.xml -g /working-dir/tmp_hcw2/Contig/contig1 -m /MFannot_data/models/HMM_models/RNA/3-rnl-other.hmm -n rnl HMMsearchCombiner -o /working-dir/tmp_hcw2/Contig/contig1-rnl.xml \ /working-dir/tmp_hcw2/RNL/5-rnl-yeast.xml \ /working-dir/tmp_hcw2/RNL/5-rnl-other.xml \ /working-dir/tmp_hcw2/RNL/3-rnl-yeast.xml \ /working-dir/tmp_hcw2/RNL/3-rnl-other.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnl.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'tRNA'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.tRNA.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.tRNA.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.tRNA.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.tRNA.B-0.MfGC.1 START --- RNAfinder -m tRNA -g 4 -d /working-dir/tmp_hcw2/Contig/contig2 -M /working-dir/tmp_hcw2/Contig/contig2-tRNA.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.tRNA.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'tRNA'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.tRNA.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.tRNA.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.tRNA.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.tRNA.B-0.MfGC.1 START --- RNAfinder -m tRNA -g 4 -d /working-dir/tmp_hcw2/Contig/contig3 -M /working-dir/tmp_hcw2/Contig/contig3-tRNA.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.tRNA.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'tRNA'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.tRNA.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.tRNA.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.tRNA.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.tRNA.B-0.MfGC.1 START --- RNAfinder -m tRNA -g 4 -d /working-dir/tmp_hcw2/Contig/contig1 -M /working-dir/tmp_hcw2/Contig/contig1-tRNA.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.tRNA.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rnpB'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rnpB.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rnpB.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rnpB.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnpB.B-0.MfGC.1 START --- RNAfinder -m rnpB -g 4 -d /working-dir/tmp_hcw2/Contig/contig2 -M /working-dir/tmp_hcw2/Contig/contig2-rnpB.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnpB.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rnpB'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rnpB.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rnpB.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rnpB.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnpB.B-0.MfGC.1 START --- RNAfinder -m rnpB -g 4 -d /working-dir/tmp_hcw2/Contig/contig3 -M /working-dir/tmp_hcw2/Contig/contig3-rnpB.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnpB.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rnpB'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rnpB.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rnpB.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rnpB.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnpB.B-0.MfGC.1 START --- RNAfinder -m rnpB -g 4 -d /working-dir/tmp_hcw2/Contig/contig1 -M /working-dir/tmp_hcw2/Contig/contig1-rnpB.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rnpB.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rrn5'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rrn5.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rrn5.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 START --- RNAfinder -m rrn5 -g 4 -d /working-dir/tmp_hcw2/Contig/contig2 -M /working-dir/tmp_hcw2/Contig/contig2-rrn5.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rrn5'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rrn5.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rrn5.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 START --- RNAfinder -m rrn5 -g 4 -d /working-dir/tmp_hcw2/Contig/contig3 -M /working-dir/tmp_hcw2/Contig/contig3-rrn5.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 END --- DEBUG: Executing external script block 'B-0' for 'rrn5'. --- COMMAND : cd '/working-dir/tmp_hcw2/Contig/err_out';/bin/bash '/working-dir/tmp_hcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1' >'/working-dir/tmp_hcw2/Contig/err_out/out.rrn5.B-0.MfGC.1' 2>'/working-dir/tmp_hcw2/Contig/err_out/err.rrn5.B-0.MfGC.1' --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 START --- RNAfinder -m rrn5 -g 4 -d /working-dir/tmp_hcw2/Contig/contig1 -M /working-dir/tmp_hcw2/Contig/contig1-rrn5.xml --- SCRIPT /working-dir/tmp_hcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 END --- 11) Adjust intron boundaries... 12) Identify start codons; identify gene fusions... 13) Find extra genes with HMM Cannot open /working-dir/tmp_hcw2/contig/contig1/contig1.faa in GetORFForLowConservedGenes