###################################################################### MFANNOT, ORGANELLAR GENOME ANNOTATION PROGRAM VERSION 1.35 Programmed by N. Beck and P. Rioux ###################################################################### ---------------------------------- General Options ---------------------------------- Masterfile used : HLJ1.assembly.mitochondrial_genome.fa New Masterfile created : HLJ1.mitochondrial_genome.mfannot.out Genetic code : 3 Logfile : HLJ1.mitochondrial_genome.mfannot.log Usage of RNAweasel The Path of configfile is : /home/travisan/public/local/soft/MFannot_data/config/.mfannot_external_programs.conf The Path of pattern file is : /home/travisan/public/local/soft/MFannot_data/config/.motsearch.pat Look in the peptide library /home/travisan/public/local/soft/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: 40 Parsing masterfile HLJ1.assembly.mitochondrial_genome.fa... Number of contigs in Masterfile : 1 Number of annotations (or comments) detected : 0 1) Translate (flip)... Making local copy of masterfile with no CRs. /home/travisan/public/local/bin/flip -m -l 40 -g 3 mf_noCr.all > /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/flip.output 2) Blast... /home/travisan/public/local/bin/makeblastdb -in /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/library.pep -dbtype prot -out /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/mf >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/blastp -outfmt 5 -matrix BLOSUM62 -db /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/mf -query /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/prot.lst -out /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/blastoutput.xml 2> /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/blasterr_1.txt 3) Parse Blast Results... 4) Select best proteins for Exonerate... 5) Annotate genes w/o introns... /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp82c17090/atp8.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp82c17090/atp8.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp82c17090/atp8.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp82c17090/atp8.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp82c17090/atp8.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp82c17090/atp8.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp82c17090/atp8.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp82c17090/atp8.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp82c17090/atp8.seq >/dev/null 2>/dev/null /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp62c179f0/atp6.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp62c179f0/atp6.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp62c179f0/atp6.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp62c179f0/atp6.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp62c179f0/atp6.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp62c179f0/atp6.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp62c179f0/atp6.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp62c179f0/atp6.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp62c179f0/atp6.seq >/dev/null 2>/dev/null /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp92c369d0/atp9.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp92c369d0/atp9.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp92c369d0/atp9.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp92c369d0/atp9.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp92c369d0/atp9.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp92c369d0/atp9.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp92c369d0/atp9.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp92c369d0/atp9.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/atp92c369d0/atp9.seq >/dev/null 2>/dev/null /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox32c177c8/cox3.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox32c177c8/cox3.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox32c177c8/cox3.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox32c177c8/cox3.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox32c177c8/cox3.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox32c177c8/cox3.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox32c177c8/cox3.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox32c177c8/cox3.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox32c177c8/cox3.seq >/dev/null 2>/dev/null DEBUG: Executing external script block 'B-0' for 'IntronI'. --- COMMAND : cd '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out';/bin/bash '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/bashcom.IntronI.B-0.MfGC.26290' >'/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/out.IntronI.B-0.MfGC.26290' 2>'/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/err.IntronI.B-0.MfGC.26290' --- SCRIPT /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/bashcom.IntronI.B-0.MfGC.26290 START --- # Setup work dir. mkdir /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/intronI cd /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/intronI RNAfinder -m IntronI -g 3 -d /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/contig1 -M /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/contig1-IntronI.xml # cd ..;rm -rf intronI --- SCRIPT /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/bashcom.IntronI.B-0.MfGC.26290 END --- 6) Intron identification... DEBUG: Executing external script block 'B-0' for 'IntronII'. --- COMMAND : cd '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out';/bin/bash '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/bashcom.IntronII.B-0.MfGC.26290' >'/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/out.IntronII.B-0.MfGC.26290' 2>'/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/err.IntronII.B-0.MfGC.26290' --- SCRIPT /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/bashcom.IntronII.B-0.MfGC.26290 START --- # Setup work dir. mkdir /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/intronII cd /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/intronII RNAfinder -m IntronII -g 3 -d /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/contig1 -M /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/contig1-IntronII.xml # cd ..;rm -rf intronII --- SCRIPT /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Contig/err_out/bashcom.IntronII.B-0.MfGC.26290 END --- 7) Annotate genes with introns... /home/travisan/public/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /home/travisan/public/local/soft/MFannot_data/models/Splice/neutral.pssm --splice5 /home/travisan/public/local/soft/MFannot_data/models/Splice/neutral.pssm --geneticcode 3 /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Exonerate/prot_for_exonerate_0_cox1 '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Exonerate/gene_for_exonerate_contig1' > /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Exonerate/exonerate_0_cox1 /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox12c1af78/cox1.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox12c1af78/cox1.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox12c1af78/cox1.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox12c1af78/cox1.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox12c1af78/cox1.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox12c1af78/cox1.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox12c1af78/cox1.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox12c1af78/cox1.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cox12c1af78/cox1.seq >/dev/null 2>/dev/null /home/travisan/public/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /home/travisan/public/local/soft/MFannot_data/models/Splice/neutral.pssm --splice5 /home/travisan/public/local/soft/MFannot_data/models/Splice/neutral.pssm --geneticcode 3 /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Exonerate/prot_for_exonerate_1_cob '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Exonerate/gene_for_exonerate_contig1' > /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Exonerate/exonerate_1_cob /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cob3b48130/cob.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cob3b48130/cob.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cob3b48130/cob.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cob3b48130/cob.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cob3b48130/cob.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cob3b48130/cob.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cob3b48130/cob.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cob3b48130/cob.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/cob3b48130/cob.seq >/dev/null 2>/dev/null /home/travisan/public/local/bin/exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --splice3 /home/travisan/public/local/soft/MFannot_data/models/Splice/neutral.pssm --splice5 /home/travisan/public/local/soft/MFannot_data/models/Splice/neutral.pssm --geneticcode 3 /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Exonerate/prot_for_exonerate_2_rps3 '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Exonerate/gene_for_exonerate_contig1' > /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Exonerate/exonerate_2_rps3 /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps33b44eb8/rps3.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps33b44eb8/rps3.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps33b44eb8/rps3.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps33b44eb8/rps3.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps33b44eb8/rps3.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps33b44eb8/rps3.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps33b44eb8/rps3.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps33b44eb8/rps3.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps33b44eb8/rps3.seq >/dev/null 2>/dev/null DEBUG: Executing external script block 'B-0' for 'IntronII'. --- COMMAND : cd '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out';/bin/bash '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/bashcom.IntronII.B-0.MfGC.26290' >'/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/out.IntronII.B-0.MfGC.26290' 2>'/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/err.IntronII.B-0.MfGC.26290' --- SCRIPT /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/bashcom.IntronII.B-0.MfGC.26290 START --- # Setup work dir. mkdir /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/intronII cd /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/intronII RNAfinder -m IntronII -g 3 -d /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/rps3.3b59c60.fasta -M /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/rps3.3b59c60-II.xml # cd ..;rm -rf intronII --- SCRIPT /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/bashcom.IntronII.B-0.MfGC.26290 END --- DEBUG: Executing external script block 'B-0' for 'IntronI'. --- COMMAND : cd '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out';/bin/bash '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/bashcom.IntronI.B-0.MfGC.26290' >'/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/out.IntronI.B-0.MfGC.26290' 2>'/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/err.IntronI.B-0.MfGC.26290' --- SCRIPT /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/bashcom.IntronI.B-0.MfGC.26290 START --- # Setup work dir. mkdir /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/intronI cd /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/intronI RNAfinder -m IntronI -g 3 -d /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/rps3.3b59c60.fasta -M /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/rps3.3b59c60-I.xml # cd ..;rm -rf intronI --- SCRIPT /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/Intron/err_out/bashcom.IntronI.B-0.MfGC.26290 END --- /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps32c2ab08/rps3.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps32c2ab08/rps3.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps32c2ab08/rps3.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps32c2ab08/rps3.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps32c2ab08/rps3.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps32c2ab08/rps3.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps32c2ab08/rps3.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps32c2ab08/rps3.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Start/rps32c2ab08/rps3.seq >/dev/null 2>/dev/null 8) Identify gene fusions... 9) Annotate mini exons... /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.seq >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.aln' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cox1_2c1af78/cox1_0.ali' -f clustal >/dev/null 2>/dev/null /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.seq >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.aln' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/cob_3b48130/cob_0.ali' -f clustal >/dev/null 2>/dev/null /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.seq >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.aln' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_3b44eb8/rps3_0.ali' -f clustal >/dev/null 2>/dev/null /home/travisan/public/local/bin/muscle -in '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.homo' -out '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.pir' >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.pir' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.sto' -f stockholm >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmbuild /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.sto >/dev/null 2>/dev/null nice -19 /home/travisan/public/local/bin/hmmalign --trim --outformat stockholm -o /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.aln /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.hmm /scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.seq >/dev/null 2>/dev/null /home/travisan/public/local/bin/umac -i '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.aln' -o '/scratch.global/gettl008/seq_processing/scerevisiae/assemblies/annotations/raw.mito/HLJ1/tmp/HMM_For_Exo/rps3_2c2ab08/rps3_0.ali' -f clustal >/dev/null 2>/dev/null ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Could not find a sequence segment in myProt containing residue number 492 STACK: Error::throw STACK: Bio::Root::Root::throw /home/travisan/public/local/lib/perl5/site_perl/5.30.2/Bio/Root/Root.pm:449 STACK: Bio::SimpleAlign::column_from_residue_number /home/travisan/public/local/lib/perl5/site_perl/5.30.2/Bio/SimpleAlign.pm:2683 STACK: main::DefineSeqOfHypprotAndPosOfIntronInAlignment /home/travisan/public/local/bin/mfannot:3491 STACK: /home/travisan/public/local/bin/mfannot:3130 -----------------------------------------------------------