testsrc/testdata/ljobs/Tcoffee#131395316639558/error.txt

   1
   2 PROGRAM: T-COFFEE (Version_8.14)
   3 -full_log       S       [0]
   4 -run_name       S       [0]
   5 -mem_mode       S       [0]     mem
   6 -extend         D       [1]     1
   7 -extend_mode    S       [0]     very_fast_triplet
   8 -max_n_pair     D       [0]     10
   9 -seq_name_for_quadruplet        S       [0]     all
  10 -compact        S       [0]     default
  11 -clean          S       [0]     no
  12 -do_self        FL      [0]     0
  13 -do_normalise   D       [0]     1000
  14 -template_file  S       [0]
  15 -template_mode  S       [0]
  16 -remove_template_file   D       [0]     0
  17 -profile_template_file  S       [0]
  18 -in             S       [0]
  19 -seq            S       [1]     fasta.in
  20 -aln            S       [0]
  21 -method_limits  S       [0]
  22 -method         S       [0]
  23 -lib            S       [0]
  24 -profile        S       [0]
  25 -profile1       S       [0]
  26 -profile2       S       [0]
  27 -pdb            S       [0]
  28 -relax_lib      D       [0]     1
  29 -filter_lib     D       [0]     0
  30 -shrink_lib     D       [0]     0
  31 -out_lib        W_F     [0]     no
  32 -out_lib_mode   S       [0]     primary
  33 -lib_only       D       [0]     0
  34 -outseqweight   W_F     [0]     no
  35 -dpa            FL      [0]     0
  36 -seq_source     S       [0]     ANY
  37 -cosmetic_penalty       D       [0]     0
  38 -gapopen        D       [0]     0
  39 -gapext         D       [0]     0
  40 -fgapopen       D       [0]     0
  41 -fgapext        D       [0]     0
  42 -nomatch        D       [0]     0
  43 -newtree        W_F     [0]     default
  44 -tree           W_F     [0]     NO
  45 -usetree        R_F     [0]
  46 -tree_mode      S       [0]     nj
  47 -distance_matrix_mode   S       [0]     ktup
  48 -distance_matrix_sim_mode       S       [0]     idmat_sim1
  49 -quicktree      FL      [0]     0
  50 -outfile        W_F     [0]     default
  51 -maximise       FL      [1]     1
  52 -output         S       [1]     clustalw
  53 -infile         R_F     [0]
  54 -matrix         S       [0]     default
  55 -tg_mode        D       [0]     1
  56 -profile_mode   S       [0]     cw_profile_profile
  57 -profile_comparison     S       [0]     profile
  58 -dp_mode        S       [0]     linked_pair_wise
  59 -ktuple         D       [0]     1
  60 -ndiag          D       [0]     0
  61 -diag_threshold D       [0]     0
  62 -diag_mode      D       [0]     0
  63 -sim_matrix     S       [0]     vasiliky
  64 -transform      S       [0]
  65 -outorder       S       [0]     input
  66 -inorder        S       [0]     aligned
  67 -seqnos         S       [0]     off
  68 -case           S       [0]     keep
  69 -cpu            D       [0]     0
  70 -maxnseq        D       [0]     1000
  71 -maxlen         D       [0]     -1
  72 -weight         S       [0]     default
  73 -seq_weight     S       [0]     t_coffee
  74 -align          FL      [1]     1
  75 -mocca          FL      [0]     0
  76 -domain         FL      [0]     0
  77 -start          D       [0]     0
  78 -len            D       [0]     0
  79 -scale          D       [0]     0
  80 -mocca_interactive      FL      [0]     0
  81 -method_evaluate_mode   S       [0]     default
  82 -evaluate_mode  S       [0]     t_coffee_fast
  83 -get_type       FL      [0]     0
  84 -clean_aln      D       [0]     0
  85 -clean_threshold        D       [1]     1
  86 -clean_iteration        D       [1]     1
  87 -clean_evaluate_mode    S       [0]     t_coffee_fast
  88 -extend_matrix  FL      [0]     0
  89 -prot_min_sim   D       [0]     0
  90 -prot_max_sim   D       [90]    90
  91 -prot_min_cov   D       [0]     0
  92 -pdb_min_sim    D       [35]    35
  93 -pdb_max_sim    D       [100]   100
  94 -pdb_min_cov    D       [50]    50
  95 -pdb_blast_server       W_F     [0]     EBI
  96 -blast          W_F     [0]
  97 -blast_server   W_F     [0]     EBI
  98 -pdb_db         W_F     [0]     pdb
  99 -protein_db     W_F     [0]     uniprot
 100 -method_log     W_F     [0]     no
 101 -struc_to_use   S       [0]
 102 -cache          W_F     [0]     use
 103 -align_pdb_param_file   W_F     [0]     no
 104 -align_pdb_hasch_mode   W_F     [0]     hasch_ca_trace_bubble
 105 -external_aligner       S       [0]     NO
 106 -msa_mode       S       [0]     tree
 107 -one2all        S       [0]
 108 -subset2all     S       [0]
 109 -lalign_n_top   D       [0]     10
 110 -iterate        D       [0]     0
 111 -trim           D       [0]     0
 112 -split          D       [0]     0
 113 -trimfile       S       [0]     default
 114 -split          D       [0]     0
 115 -split_nseq_thres       D       [0]     0
 116 -split_score_thres      D       [0]     0
 117 -check_pdb_status       D       [0]     0
 118 -clean_seq_name D       [0]     0
 119 -seq_to_keep    S       [0]
 120 -dpa_master_aln S       [0]
 121 -dpa_maxnseq    D       [0]     0
 122 -dpa_min_score1 D       [0]
 123 -dpa_min_score2 D       [0]
 124 -dpa_keep_tmpfile       FL      [0]     0
 125 -dpa_debug      D       [0]     0
 126 -multi_core     S       [0]     templates_jobs_relax_msa
 127 -n_core         D       [1]     1
 128 -lib_list       S       [0]
 129 -prune_lib_mode S       [0]     5
 130 -tip            S       [0]     one
 131 -rna_lib        S       [0]
 132 -no_warning     D       [0]     0
 133 -run_local_script       D       [0]     0
 134 -plugins        S       [0]     default
 135 -proxy          S       [0]     unset
 136 -email          S       [0]
 137 -clean_overaln  D       [0]     0
 138 -overaln_param  S       [0]
 139 -overaln_mode   S       [0]
 140 -overaln_model  S       [0]
 141 -overaln_threshold      D       [0]     0
 142 -overaln_target D       [0]     0
 143 -overaln_P1     D       [0]     0
 144 -overaln_P2     D       [0]     0
 145 -overaln_P3     D       [0]     0
 146 -overaln_P4     D       [0]     0
 147 -exon_boundaries        S       [0]
 148
 149 INPUT FILES
 150         Input File (S) fasta.in  Format fasta_seq
 151         Input File (M) proba_pair
 152
 153 INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
 154   Input File fasta.in  Seq Sequence0 Length  113 type PROTEIN Struct Unchecked
 155   Input File fasta.in  Seq Sequence1 Length   52 type PROTEIN Struct Unchecked
 156   Input File fasta.in  Seq Sequence2 Length   53 type PROTEIN Struct Unchecked
 157   Input File fasta.in  Seq Sequence3 Length   80 type PROTEIN Struct Unchecked
 158   Input File fasta.in  Seq Sequence4 Length   45 type PROTEIN Struct Unchecked
 159   Input File fasta.in  Seq Sequence5 Length   56 type PROTEIN Struct Unchecked
 160   Input File fasta.in  Seq Sequence6 Length   62 type PROTEIN Struct Unchecked
 161   Input File fasta.in  Seq Sequence7 Length   40 type PROTEIN Struct Unchecked
 162   Input File fasta.in  Seq Sequence8 Length   61 type PROTEIN Struct Unchecked
 163
 164 COMPUTE PAIRWISE SIMILARITY [dp_mode: ] [distance_matrix_mode: ktup][Similarity Measure: idmat_sim1]
 165
 166         Seq: Sequence0
 167         Seq: Sequence1
 168         Seq: Sequence2
 169         Seq: Sequence3
 170         Seq: Sequence4
 171         Seq: Sequence5
 172         Seq: Sequence6
 173         Seq: Sequence7
 174         Seq: Sequence8
 175
 176 READ/MAKE LIBRARIES:[2]
 177
 178         proba_pair [method]
 179
 180                 [Submit   Job][TOT=   36][  0 %][ELAPSED TIME:    0 sec.]
 181                 [Submit   Job][TOT=   36][  5 %][ELAPSED TIME:    0 sec.]
 182                 [Submit   Job][TOT=   36][  8 %][ELAPSED TIME:    0 sec.]
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 188                 [Submit   Job][TOT=   36][ 25 %][ELAPSED TIME:    0 sec.]
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 195                 [Submit   Job][TOT=   36][ 44 %][ELAPSED TIME:    0 sec.]
 196                 [Submit   Job][TOT=   36][ 47 %][ELAPSED TIME:    0 sec.]
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 203                 [Submit   Job][TOT=   36][ 66 %][ELAPSED TIME:    0 sec.]
 204                 [Submit   Job][TOT=   36][ 69 %][ELAPSED TIME:    0 sec.]
 205                 [Submit   Job][TOT=   36][ 72 %][ELAPSED TIME:    0 sec.]
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 208                 [Submit   Job][TOT=   36][ 80 %][ELAPSED TIME:    0 sec.]
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 212                 [Submit   Job][TOT=   36][ 91 %][ELAPSED TIME:    0 sec.]
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 214                 [Submit   Job][TOT=   36][ 97 %][ELAPSED TIME:    0 sec.]
 215                 [Submit   Job][TOT=   36][100 %][ELAPSED TIME:    0 sec.]
 216
 217 MANUAL PENALTIES: gapopen=0 gapext=0
 218
 219         Library Total Size: [6542]
 220
 221 Library Relaxation:[6542] --->[5767]
 222
 223         #### File Type=     WEIGHT Format=  tc_weight Name= no | NOT PRODUCED [WARNING:T-COFFEE:Version_8.14]
 224
 225
 226 WEIGHTED MODE:t_coffee
 227
 228         Sequence0 1.08
 229         Sequence1 0.82
 230         Sequence2 1.07
 231         Sequence3 1.08
 232         Sequence4 1.05
 233         Sequence5 0.82
 234         Sequence6 0.95
 235         Sequence7 1.05
 236         Sequence8 1.07
 237
 238
 239 MAKE GUIDE TREE
 240         [MODE=nj][DONE]
 241
 242 PROGRESSIVE_ALIGNMENT [Tree Based]
 243
 244         Group   10: [Group    8 (   1 seq)] with [Group    5 (   1 seq)]-->[Score=  31][Len=   48][PID:23942]
 245         Group   11: [Group   10 (   2 seq)] with [Group    3 (   1 seq)]-->[Score=  32][Len=   55][PID:23942]
 246         Group   12: [Group    9 (   1 seq)] with [Group   11 (   3 seq)]-->[Score=  34][Len=   63][PID:23942]
 247         Group   13: [Group   12 (   4 seq)] with [Group    4 (   1 seq)]-->[Score=  11][Len=   95][PID:23942]
 248         Group   14: [Group    6 (   1 seq)] with [Group    2 (   1 seq)]-->[Score=  80][Len=   56][PID:23942]
 249         Group   15: [Group    7 (   1 seq)] with [Group   14 (   2 seq)]-->[Score=  63][Len=   62][PID:23942]
 250         Group   16: [Group   15 (   3 seq)] with [Group   13 (   5 seq)]-->[Score=  12][Len=  102][PID:23942]
 251         Group   17: [Group    1 (   1 seq)] with [Group   16 (   8 seq)]-->[Score=  11][Len=  142][PID:23942]
 252
 253
 254
 255 OUTPUT RESULTS
 256         #### File Type= GUIDE_TREE Format=     newick Name= fasta.dnd
 257         #### File Type=        MSA Format=   clustalw Name= fasta.clustalw
 258
 259
 260 # TIP :See The Full Documentation on www.tcoffee.org
 261 # TIP  1:  Get the most accurate protein alignments with: t_coffee <yourseq> -special_mode accurate [Slow]
 262 # TIP 10:  -usetree=<file> to use your own guide tree
 263
 264 # Command Line: /homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee -output=clustalw -seq=fasta.in -n_core=1  [PROGRAM:T-COFFEE]
 265 # T-COFFEE Memory Usage: Current= 11.932 Mb, Max= 13.916 Mb
 266 # T-COFFEE CPU Usage: 250 millisec
 267 # Results Produced with T-COFFEE (Version_8.14)
 268 # T-COFFEE is available from http://www.tcoffee.org