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tGtB&t6vt.vt&t$<$t$<$~uZf1ҋ]Ћu}]Í&CD$<$QzE <$D$Z뱍&FD$<$tE <$D$kzE <$D$_UBP G1҃K E 4$D$;HvE 4$D$NvE 4$D$)뮍vE 4$D$u붍vE 4$D$.'Q;vE 4$D$kUB aXOK&vE 4$D$농vE 4$D$9믍vE 4$D$WE 4$D$uUEu]D$w$)!u]u]Ít&D$ E D$D$0$!4$ 1uUEu]D$w$ u]u]Ít&D$ E D$D$0$!4$g 1uUM E]ʃÍt&UM ʃU ]fUM ʃU]Ít&UM ʃU0]ÐU]Ít&'UWVSO9( )t$1ED$E D$E$9rރ [^_]Ë$ÐUStfЋu[]ÐUS[ì' Y[ Usage: prodigal [-a ] [-c] [-g ] [-o ] [-s ] < > -h: Print help menu. -a: Write protein translations to the selected -c: Closed ends. Do not allow genes to run off -g: Specify a translation table to use (default -m: Treat runs of n's as masked sequence and do -n: Bypass the Shine-Dalgarno trainer and force -o: Select output format (gbk, gff, or sco) -s: Write all potential genes (with scores) to -t: Write a training file (if none exists); the specified training file. -v: Print version number and exit. Single sequence : prodigal < fasta.seq > Training on draft: cat fasta_seqs.* | prodigal Running on draft: prodigal -t my.trn < prodigal -t my.trn < Prodigal V1.20: September, 2009 Usage: prodigal [-a ] [-c] [-g ] Do 'prodigal -h' for more information. Malloc failed on sequence/orfs -g, -s, -t, and -o options require parameters.Invalid translation table specified.Invalid output format specified.------------------------------------- PRODIGAL v1.20 [September, 2009] Univ of Tenn / Oak Ridge National Lab Doug Hyatt, Loren Hauser, et al. Reading in training data from file %s...error, cannot force non-SD finder with a trainingwarning, user-specified translation table does not match the one in the specified training file! Sequence read failed (file must be Fasta, Genbank, orSequence must be 1000 characters (only %d bp seq created, %.2f pct GC Locating all potential starts and stops...Looking for GC bias in different frames...Malloc failed on gc frame plot frame bias scores: %.2f %.2f %.2f Building initial set of genes to train from...Creating coding model and scoring nodes...Examining upstream regions and training starts...Writing data to training file %s...Building set of genes from statistics... [-h] [-m] [-n] [-t ] [-v] edges. 11). not build genes across them. the program to scan for motifs. the selected file. otherwise, read and use my.genes -t my.trn fasta_seqs.1 fasta_seqs.2 etc. %s Unknown option. file already created! error! done! Reading in the sequence... EMBL format). %d read). %d bp read, %.2f pct GC 0 nodes, exiting... %d nodes ffffff@Bwarning, max # of genes exceeded, truncating... Error writing translation file. >Prodigal Gene %d # %d # %d # 1 >Prodigal Gene %d # %d # %d # -1 gene_prodigal=%d|1|f|y|y|3|0|%d|%d|%d|%d|-1|-1|1.0 CDS complement(%s..%s) gene_prodigal=%d|1|r|y|y|3|0|%d|%d|%d|%d|-1|-1|1.0 w<%d>%d CDS %s..%s >%d_%d_%d_+ SEQ Prodigal CDS %d %d . + 0 >%d_%d_%d_- SEQ Prodigal CDS %d %d . - 0 z333333ÿError writing start file. Spacer RBSScr UpsScr TypeScr %d %d + %.2f %.2f %.2f %s %d %d - %.2f %.2f %.2f %s %s %s %.2f None None %.2f %s %dbp %.2f %.2f %.2f Beg End Std Total CodPot StrtSc Codon RBSMot ?@pAp>>@@@zDBfD?@zC AD B@?333333?Gz????Warning: saw non-sequence line longer than %d chars, sequence might not be read Warning: saw second sequence header (only analyzing the first sequence) Error: gap size in gbk file can't exceed lineError: saw too many regions of 'N''s in the Sequence too long (max %d permitted). correctly. ORIGINExpandgap size. sequence. @@@AA0A@A`Awbrb;|4PzR| @AB 84ZAB C6  N^n~·އ.GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]GCC: (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291]@"$" $ > $ > 4: ; I?  &IU%% $ > : ; I$ > .? : ; ' @.? : ; ' @: ; I 4: ; I  4: ; I  I &I I!' I4: ; I? < U%W2 ../sysdeps/i386/elfstart.S@3!4=%" YZ!"\[# init.cl /usr/src/packages/BUILD/glibc-2.9/cc-nptl/csu../sysdeps/genericcrti.Sinitfini.c!/!=Z!gg// R`U cXhj0~;O.QIbXop-@9` <RH@g`g\gZ%*<@ MMU`wp7x01H}h@fje0H`0/@5'/M/@ gEP) Vdg`Ln`..u K|pP<1\0 0HgKY 02``,@Y?O^ hu@@0K `*Yinit.cinitfini.ccrtstuff.c__CTOR_LIST____DTOR_LIST____JCR_LIST____do_global_dtors_auxcompleted.5719dtor_idx.5721frame_dummy__CTOR_END____FRAME_END____JCR_END____do_global_ctors_auxmain.cgene.cdprog.cnode.csequence.ctraining.cbitmap.celf-init.c_GLOBAL_OFFSET_TABLE___init_array_end__init_array_start_DYNAMICdata_startsprintf@@GLIBC_2.0read_training_filerecord_overlapping_startsscore_nodesdmincompare_nodesdprog__libc_csu_finiqsort@@GLIBC_2.0train_starts_sd_startmer_textis_ashine_dalgarno_mmshine_dalgarno_exactdmax__gmon_start___Jv_RegisterClassesscore_connection_fp_hwupdate_motif_countscalc_mer_bg_finipow@@GLIBC_2.0fgets@@GLIBC_2.0eliminate_bad_genesmemset@@GLIBC_2.0__libc_start_main@@GLIBC_2.0is_startadd_nodes_IO_stdin_usedstrtol@@GLIBC_2.0free@@GLIBC_2.0max_frstart_textfind_best_upstream_motif__data_startfflush@@GLIBC_2.0amino_lettercross_maskfclose@@GLIBC_2.1stderr@@GLIBC_2.0add_genesaminofopen@@GLIBC_2.1clearsettweak_final_starts__dso_handle__DTOR_END____libc_csu_inithelpprintf@@GLIBC_2.0write_start_fileis_stopcount_upstream_compositionversionis_crbs_scorefwrite@@GLIBC_2.0fprintf@@GLIBC_2.0strstr@@GLIBC_2.0write_training_filecalc_dicodon_geneis_g__bss_startmalloc@@GLIBC_2.0record_gc_biasiminprint_genesmer_ndxfputc@@GLIBC_2.0testraw_coding_scorestdin@@GLIBC_2.0is_ttgrframeis_atg_endlog@@GLIBC_2.0calc_most_gc_framercom_sequsagesscanf@@GLIBC_2.0is_ttoggletrain_starts_nonsdfread@@GLIBC_2.0is_gtgstopcmp_nodesread_seq_edatawrite_translationsbuild_coverage_mapexit@@GLIBC_2.0intergenic_mod__i686.get_pc_thunk.bxscore_upstream_compositionmainis_gc_initdetermine_sd_usageamino_num