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OUTPUT: -pir FILE Write out MSA in PIR format. -clustal FILE Write out MSA in CLUSTAL format. -po FILE Write out MSA in PO format. -preserve_seqorder Write out MSA with sequences in their input order. -printmatrix LETTERS Print score matrix to stdout. -best Restrict MSA output to heaviest bundles (PIR only). -v Run in verbose mode (e.g. output gap penalties). NOTE: One of the -read_fasta, -read_msa, or -read_msa_list arguments must be used, since a sequence or alignment file is required. For more information, see http://www.bioinformatics.ucla.edu/poa. -tolower-toupper-v-best-hb-printmatrix-read_msa-read_msa2-read_msa_list-pir-clustal-po-preserve_seqorder-hbmin-fuse_all-do_global-read_pairscores-do_progressive-subset-subset2-remove-remove2-read_fastaError: The -read_po_list and -read_po flags cannot be used at the same time. Exiting.$Revision: 1.2.2.9 $main.cError: Each -subset/-remove flag must have a corresponding -read_po flag. Exiting.Error: The -subset and -remove flags cannot be used at the same time. Exiting.because none specifiedError reading matrix file %s. ExitingX-Gap Penalties (Open, Aff1, Aff2; LTrunc, LDecay): %d %d %d %d %d X-Gap Penalties (0, 1, 2, ...): %d ... Y-Gap Penalties (Open, Aff1, Aff2; LTrunc, LDecay): %d %d %d %d %d Y-Gap Penalties (0, 1, 2, ...): %s, line %d: *** out of memory input_seqsUnable to meet request: %s[%d] requested %d x %d bytes ...Read %d sequences from MSA file %s... ...Read %d sequences from second MSA file %s... r...Read %d sequences from PO list entry %s... Unable to meet request: %s %sError reading PO list file %s. ExitingCouldn't open sequence file %s. ExitingError reading sequence file %s. Exiting...Read %d sequences from sequence file %s... No input sequences were provided; use one of the -read_ flags. Exiting.w...Wrote %d sequences to PO file %s... *** Could not save PO file %s. Exiting....Wrote %d sequences to FASTA-PIR file %s... *** Could not save FASTA-PIR file %s. Exiting....Wrote %d sequences to CLUSTAL file %s... *** Could not save CLUSTAL file %s. Exiting.Couldn't open MSA file %s. Exiting.Couldn't open subset file %s. Exiting.MSA file %s, filtered with subset file %s, couldn't be read or contains no sequences. Exiting.MSA file %s couldn't be read or contains no sequences. Exiting.black_flagunknownCRASHDIEDEXCEPTIONBAD_DATAWARNINGDEBUG black_flag: %s %s:%s %s %s,%d %s end_black_flag HANDLE_CRASHNOCOREblack_flag.c%s, line %d: *** out of memory Program_nameUnable to meet request: %s[%d] requested %d x %d bytes rCan't open alignment matrix from %s $Revision: 1.2.2.2 $seq_util.cGAP-TRUNCATION-LENGTH=%dGAP-DECAY-LENGTH=%dGAP-PENALTIES=%d %d %dGAP-PENALTIES-X=%d %d %d%d%nMissing score value for pair %c:%c5.23Missing or unknown sequence symbol: %c1.5%s, line %d: *** out of memory m->gap_penalty_xUnable to meet request: %s[%d] requested %d x %d bytes m->gap_penalty_y %c%3d6-666$666666666666666666666666-666$666666666666%s %[^ ]untitled>%s %s %.60s VERSION=CLUSTALUnable to determine MSA file type... trying CLUSTAL. $Revision: 1.1.2.3 $msa_format.cNo data in MSA file. %s %[^ ]Error: Trouble reading CLUSTAL-formatted file near line %d: >>> %s<<< Bailing out. %s, line %d: *** out of memory seq_namesUnable to meet request: %s requested %d x %d bytes seq_titlesaln_mat aln_lengthsError: Trouble reading CLUSTAL-formatted file at line %d: >>> %s<<< Sequence name (%s) does not match expected sequence name (%s). Bailing out. aln_mat[curr_seq]>%s %[^ ]Error: Trouble reading PIR-formatted file near line %d (no sequence name?): >>> %s<<< Bailing out. %[^ ]Error: Trouble reading PIR-formatted file near line %d (no preceding '>seqname' line?): >>> %s<<< Bailing out. column_idsUnable to meet request: %s[%d] res_idscolumn_ids[i]res_ids[i]consens_rowlposeqlposeq->sequencecurr_seqcurr_seq->sequenceal_xal_ykeep_seqSOURCENAME=%[^ ]%*[ ]Exceeded memory bound: %d Exiting! $Revision: 1.2.2.9 $buildup_lpo.c%s, line %d: *** out of memory tempUnable to meet request: %s[%d] requested %d x %d bytes %s maximum identity %3.1f%% %.0f/%d Badj_scorescore_listinvalid sequence pair, not found: %s,%sSaving score from file %d (%s), %d (%s) : %.2f Unable to meet request: %s %s %s %lfSaving alignment score %d (%s), %d (%s) : %.2f Performing iterative alignment... seq_clusterseq_id_in_clustercluster_sizeinitial_nseqrError reading pair score file %s. ExitingunspecifiedError generating pair scores (file %s). ExitingFusing cluster %d (%s, nseq=%d) --> %d (%s, nseq=%d)... score %.2f perm%d lpo.c%s, line %d: *** out of memory seq->letterUnable to meet request: %s[%d] requested %d x %d bytes seq->source_seq[i].seq_to_poseq->source_seq[i].po_to_seqseq->source_seq[i].sequenceseq->source_seqUnable to meet request: %s untitledlistlist->morenew_s->moremapinvmapBad argument! 'perm' must be a permutation of [0,%d] 1.1do_fusenew_seqnew_xnew_ynew_lpox_to_yseq_xheaviest_bundle.c%s, line %d: *** out of memory pathUnable to meet request: %s[%d] requested %d x %d bytes scorecontains_posbest_pathbundle_count/hb_weight=assigned weight=%d to %s hb_weight zero or unreadable: %s Ignored$Revision: 1.2 $CONSENS%dconsensus produced by heaviest_bundle, containing %d seqs*** WARNING: bundling ended prematurely after %d bundles. No sequences fit inside this last bundle. A total of %d sequences incuding consensus were bundled. VERSION=LPO.0.1 NAME=%s TITLE=%s LENGTH=%d SOURCECOUNT=%d SOURCENAME=%s SOURCEINFO=%d %d %d %d %s %c:L%dS%dA%dlpo_format.c%s, line %d: *** out of memory seqUnable to meet request: %s[%d] requested %d x %d bytes VERSION=%s NAME=%[^ ] TITLE=%[^ ] LENGTH=%d SOURCECOUNT=%dseq->letterseq->source_seqUnable to meet request: %s pos_count SOURCENAME=%[^ ] SOURCEINFO=%d %d %d %d%*[ ]%[^ ] %c:%diseq_compactlast_posmatch_posSOURCENAME=%[^ ] link_listpos_compactring_oldseq_pospinclude_in_save>%s %s %s%cCLUSTAL W (1.74) multiple sequence alignment untitledcreate_seq.c%s, line %d: *** out of memory *p_seqUnable to meet request: %s[%d] requested %d x %d bytes Unable to meet request: %s numeric_data.c%s, line %d: *** out of memory source_seq->dataUnable to meet request: %s[%d] requested %d x %d bytes Unable to meet request: %s data->data*** could not find dataset %s for seq %s. Exiting $Revision: 1.2 $>%s NUMERIC_DATA=%s %sError! NUMERIC_DATA %s, sequence %s does not exist. Skipping. NUMERIC_DATA %s already exists on sequence %s. Overwriting. %lfstringptr.c%s, line %d: *** out of memory s2_tempUnable to meet request: %s[%d] requested %d x %d bytes s1->pUnable to meet request: %s align_lpo_po2.c%s, line %d: *** out of memory node_typeUnable to meet request: %s[%d] requested %d x %d bytes refs_from_righttmpleft_linksleft_links[i]x_aly_alnext_gap_arraynext_perp_gap_arraymovemove[i]init_col_scorescore_rowsscore_rows[-1]score_rows[i]Bounds exceeded! best_x,best_y:%d,%d len:%d,%d 1.1aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): globallocalbest %s score = %d @ (%d %d) . 0  `T<ooo.>N^n~Ίފ.>N^n~΋ދ.>N^n~ЙۙGCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)GCC: (GNU) 4.0.2 20050901 (prerelease) (SUSE Linux)"40 %{hL#s0 ܨ  , \6̸'JdW`*{(81)#0_chain D#4_fileno"##8_flags2&##<_old_offset(e#@_cur_column,#D_vtable_offset-#F_shortbuf.J#G_lock2Z#H_offset;#L__pad1A#T__pad2B#X_modeD##\_unused2F`#` _IO_lock_t >_IO_marker  _next># _sbufD# _pos## Z p3double&black_flag#Ubug_level#usourcefileu sourceline#usourcefile_revisionulast_line#error_names&u\ 6~handle_crashC6UsigcodeB#ucrash_modeDu|handle_crash_initV#6Ucrash_funUuiX#u|signal_typeYuh #iblack_flag_init_argsiUnargh#uarghiu Fhuij#uxlenj#u|black_flag_initzܨUprognameyuFyu stderrD ERRTXT Program_name Program_version Already_reported_crash# J ܨGNU C 4.0.2 20050901 (prerelease) (SUSE Linux)seq_util.c/mnt/hgfs/notredame/untared_distributions/T-COFFEE_distribution_Version_6.84/Downloads/distributions/poa/poaV2[unsigned charshort unsigned intlong unsigned intsigned charshort intintlong long intlong long unsigned int__quad_t;(__off_trlong int__off64_tS[charFILE.h._flags !#_IO_read_ptr#_IO_read_end#_IO_read_base# _IO_write_base#_IO_write_ptr#_IO_write_end#_IO_buf_base#_IO_buf_end# _IO_save_base#$_IO_backup_base#(_IO_save_end#,_markersH#0_chain N#4_fileno"!#8_flags2&!#<_old_offset(c#@_cur_column,#D_vtable_offset-#F_shortbuf.T#G_lock2d#H_offset;~#L__pad1A#T__pad2B#X_modeD!#\_unused2Fj#` _IO_lock_t H_IO_marker  _nextH# _sbufN# _pos!# d z3doubleLPOScore_T!ResidueScore_T"float!41 nsymbol"!# symbol## score$ # best_match%# gap_penalty_set'5# trunc_gap_length(!# decay_gap_length)!# gap_penalty_x+K# gap_penalty_y+K# max_gap_length,!# nfreq.!# freq_symbol/# freq0Q#   5! K aResidueScoreMatrix_T1shuffle_seq ܨ6Ulen !useq u randseq ui!utj!uxcuindex_symbols'6Unseq%!useq%u out%unsymbs&!usymbols&ui(!utj(!uxk(!u|best_match_qsort_cmp>!&Uvoid_a=zuvoid_b=zu a?uxb?u|read_score_matrixS!&1UfilenameRumRu iT!uTjT!uPkT!uLnsymbT!uXfound_symbol_lineT!u\isymbT!u`lineUuwdna_codesU uuifileV uddec_xuhdec_yupa    print_score_matrix1sUifile umu subsetޖui!uli_m!upj!utj_m!uxnsubset!u|, limit_residues!sUsequsymbolu i!utlen!uxnreplace!u|h complementary_baseBUbaseu| reverse_complementBUsequi!upj!utc u{stderrN ERRTXT Program_nameProgram_versionScore_matrix_row;N ]=ʸGNU C 4.0.2 20050901 (prerelease) (SUSE Linux)fasta_format.c/mnt/hgfs/notredame/untared_distributions/T-COFFEE_distribution_Version_6.84/Downloads/distributions/poa/poaV2qunsigned charshort unsigned intlong unsigned intsigned charshort intintlong long intlong long unsigned int__quad_t;,__off_tvlong int__off64_tWqcharFILE.._flags %#_IO_read_ptr#_IO_read_end#_IO_read_base# 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u}pu|tmp_sequ} r   write_fastaPUʸUifileOw unameOu OuseqOujQ%uxProgram_nameProgram_versionc%d̸GNU C 4.0.2 20050901 (prerelease) (SUSE Linux)msa_format.c/mnt/hgfs/notredame/untared_distributions/T-COFFEE_distribution_Version_6.84/Downloads/distributions/poa/poaV2unsigned charshort unsigned intlong unsigned intsigned charshort intintlong long intlong long unsigned int__quad_t;*__off_ttlong int__off64_tUcharFILE.H._flags ##_IO_read_ptr#_IO_read_end#_IO_read_base# _IO_write_base#_IO_write_ptr#_IO_write_end#_IO_buf_base#_IO_buf_end# _IO_save_base#$_IO_backup_base#(_IO_save_end#,_markersU#0_chain [#4_fileno"##8_flags2&##<_old_offset(e#@_cur_column,#D_vtable_offset-#F_shortbuf.a#G_lock2q#H_offset;#L__pad1A#T__pad2B#X_modeD##\_unused2Fw#`  _IO_lock_t U_IO_marker  _nextU# _sbuf[# _pos##q3doublevoidptrLPOLetterRef_T#LPOScore_T#ResidueScore_T" &LPOLetterSource_S ' iseq)## ipos+# more-&#LPOLetterSource_T0 LPOLetterLink_S 5 ipos7# score:# more=#ELPOLetterLink_T@E 6LPOLetter_S4I leftK# rightM# 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