testsrc/testdata/jobs/@Tcoffee#9974534735170965/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]     4
 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: 10 SEQUENCES  [PROTEIN]
 154   Input File fasta.in  Seq Sequence0 Length  313 type PROTEIN Struct Unchecked
 155   Input File fasta.in  Seq Sequence1 Length  965 type PROTEIN Struct Unchecked
 156   Input File fasta.in  Seq Sequence2 Length  492 type PROTEIN Struct Unchecked
 157   Input File fasta.in  Seq Sequence3 Length 1057 type PROTEIN Struct Unchecked
 158   Input File fasta.in  Seq Sequence4 Length  577 type PROTEIN Struct Unchecked
 159   Input File fasta.in  Seq Sequence5 Length 1124 type PROTEIN Struct Unchecked
 160   Input File fasta.in  Seq Sequence6 Length  794 type PROTEIN Struct Unchecked
 161   Input File fasta.in  Seq Sequence7 Length  326 type PROTEIN Struct Unchecked
 162   Input File fasta.in  Seq Sequence8 Length  402 type PROTEIN Struct Unchecked
 163   Input File fasta.in  Seq Sequence9 Length  482 type PROTEIN Struct Unchecked
 164
 165 COMPUTE PAIRWISE SIMILARITY [dp_mode: ] [distance_matrix_mode: ktup][Similarity Measure: idmat_sim1]
 166
 167         Seq: Sequence0
 168         Seq: Sequence1
 169         Seq: Sequence2
 170         Seq: Sequence3
 171         Seq: Sequence4
 172         Seq: Sequence5
 173         Seq: Sequence6
 174         Seq: Sequence7
 175         Seq: Sequence8
 176         Seq: Sequence9
 177
 178 READ/MAKE LIBRARIES:[2]
 179
 180         proba_pair [method]
 181
 182         Multi Core Mode: 4 processors [subset]
 183
 184                 [Submit   Job][TOT=   12][  0 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 16 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 25 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 33 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 41 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 50 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 58 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 66 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 75 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 83 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=   12][ 91 %][ELAPSED TIME:    1 sec.]\r              [Submit   Job][TOT=   12][100 %][ELAPSED TIME:    1 sec.]
 185 MANUAL PENALTIES: gapopen=0 gapext=0
 186
 187         Library Total Size: [83014]
 188
 189 Library Relaxation: Multi_proc [4]
 190                 [Submit   Job][TOT=20753][  0 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][  1 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][  2 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][  3 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][  4 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][  5 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][  6 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][  7 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][  8 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][  9 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 10 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 11 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 12 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 13 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 14 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 15 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 16 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 17 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 18 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 19 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 20 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 21 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 22 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 23 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 24 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 25 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 26 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 27 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 28 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 29 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 30 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 31 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 32 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 33 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 34 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 35 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 36 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 37 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 38 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 39 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 40 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 41 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 42 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 43 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 44 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 45 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 46 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 47 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 48 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 49 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 50 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 51 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 52 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 53 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 54 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 55 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 56 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 57 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 58 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 59 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 60 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 61 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 62 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 63 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 64 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 65 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 66 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 67 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 68 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 69 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 70 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 71 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 72 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 73 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 74 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 75 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 76 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 77 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 78 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 79 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 80 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 81 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 82 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 83 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 84 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 85 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 86 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 87 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 88 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 89 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 90 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 91 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 92 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 93 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 94 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 95 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 96 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 97 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 98 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][ 99 %][ELAPSED TIME:    0 sec.]\r              [Submit   Job][TOT=20753][100 %][ELAPSED TIME:    0 sec.]
 191 Total Relaxation: [83014]--->[53572] Entries
 192
 193         #### File Type=     WEIGHT Format=  tc_weight Name= no | NOT PRODUCED [WARNING:T-COFFEE:Version_8.14]
 194
 195
 196 WEIGHTED MODE:t_coffee
 197
 198         Sequence0 1.05
 199         Sequence1 1.01
 200         Sequence2 1.00
 201         Sequence3 0.93
 202         Sequence4 1.06
 203         Sequence5 0.98
 204         Sequence6 0.94
 205         Sequence7 0.99
 206         Sequence8 1.05
 207         Sequence9 1.00
 208
 209
 210 MAKE GUIDE TREE
 211         [MODE=nj][DONE]
 212
 213 PROGRESSIVE_ALIGNMENT [Tree Based]
 214
 215         Group   13: [Group    8 (   1 seq)] with [Group    6 (   1 seq)]-->[Score=   2][Len= 1157][PID:29128]
 216         Group   11: [Group    7 (   1 seq)] with [Group    4 (   1 seq)]-->[Score=  27][Len= 1083][PID:29126]
 217         Group   14: [Group   10 (   1 seq)] with [Group   13 (   2 seq)]-->[Score=   4][Len= 1173][PID:29128]
 218         Group   12: [Group   11 (   2 seq)] with [Group    3 (   1 seq)]-->[Score=   8][Len= 1123][PID:29126]
 219         Group   15: [Group   14 (   3 seq)] with [Group    2 (   1 seq)]-->[Score=  13][Len= 1239][PID:29128]
 220         Group   17: [Group   16 (   2 seq)] with [Group   15 (   4 seq)]-->[Score=   2][Len= 1262][PID:29127][Forked]
 221         Group   18: [Group   17 (   6 seq)] with [Group   12 (   3 seq)]-->[Score=   4][Len= 1612][PID:29108][Forked]
 222         Group   19: [Group    5 (   1 seq)] with [Group   18 (   9 seq)]-->[Score=   3][Len= 1655][PID:29108]
 223
 224
 225
 226 OUTPUT RESULTS
 227         #### File Type= GUIDE_TREE Format=     newick Name= fasta.dnd
 228         #### File Type=        MSA Format=   clustalw Name= fasta.clustalw
 229
 230
 231 # TIP :See The Full Documentation on www.tcoffee.org
 232 # TIP  1:  Get the most accurate protein alignments with: t_coffee <yourseq> -special_mode accurate [Slow]
 233 # TIP  2:  Change the Width of your MSA with the environement variable ALN_LINE_LENGTH (all formats)
 234
 235 # 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=4  [PROGRAM:T-COFFEE]
 236 # T-COFFEE Memory Usage: Current= 19.700 Mb, Max= 28.281 Mb
 237 # T-COFFEE CPU Usage: 10 millisec
 238 # Results Produced with T-COFFEE (Version_8.14)
 239 # T-COFFEE is available from http://www.tcoffee.org