X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Ftestdata%2Fljobs%2FTcoffee%23131395316639558%2Ferror.txt;fp=testsrc%2Ftestdata%2Fljobs%2FTcoffee%23131395316639558%2Ferror.txt;h=cbd7981ebd0edf459706271451bdf72ec10bcf20;hb=7a5ab825edefa83e8c063359dd86a52dee66b8ef;hp=0000000000000000000000000000000000000000;hpb=451b60b868fc003d2b02a6f453461f365eb83f62;p=jabaws.git diff --git a/testsrc/testdata/ljobs/Tcoffee#131395316639558/error.txt b/testsrc/testdata/ljobs/Tcoffee#131395316639558/error.txt new file mode 100644 index 0000000..cbd7981 --- /dev/null +++ b/testsrc/testdata/ljobs/Tcoffee#131395316639558/error.txt @@ -0,0 +1,268 @@ + +PROGRAM: T-COFFEE (Version_8.14) +-full_log S [0] +-run_name S [0] +-mem_mode S [0] mem +-extend D [1] 1 +-extend_mode S [0] very_fast_triplet +-max_n_pair D [0] 10 +-seq_name_for_quadruplet S [0] all +-compact S [0] default +-clean S [0] no +-do_self FL [0] 0 +-do_normalise D [0] 1000 +-template_file S [0] +-template_mode S [0] +-remove_template_file D [0] 0 +-profile_template_file S [0] +-in S [0] +-seq S [1] fasta.in +-aln S [0] +-method_limits S [0] +-method S [0] +-lib S [0] +-profile S [0] +-profile1 S [0] +-profile2 S [0] +-pdb S [0] +-relax_lib D [0] 1 +-filter_lib D [0] 0 +-shrink_lib D [0] 0 +-out_lib W_F [0] no +-out_lib_mode S [0] primary +-lib_only D [0] 0 +-outseqweight W_F [0] no +-dpa FL [0] 0 +-seq_source S [0] ANY +-cosmetic_penalty D [0] 0 +-gapopen D [0] 0 +-gapext D [0] 0 +-fgapopen D [0] 0 +-fgapext D [0] 0 +-nomatch D [0] 0 +-newtree W_F [0] default +-tree W_F [0] NO +-usetree R_F [0] +-tree_mode S [0] nj +-distance_matrix_mode S [0] ktup +-distance_matrix_sim_mode S [0] idmat_sim1 +-quicktree FL [0] 0 +-outfile W_F [0] default +-maximise FL [1] 1 +-output S [1] clustalw +-infile R_F [0] +-matrix S [0] default +-tg_mode D [0] 1 +-profile_mode S [0] cw_profile_profile +-profile_comparison S [0] profile +-dp_mode S [0] linked_pair_wise +-ktuple D [0] 1 +-ndiag D [0] 0 +-diag_threshold D [0] 0 +-diag_mode D [0] 0 +-sim_matrix S [0] vasiliky +-transform S [0] +-outorder S [0] input +-inorder S [0] aligned +-seqnos S [0] off +-case S [0] keep +-cpu D [0] 0 +-maxnseq D [0] 1000 +-maxlen D [0] -1 +-weight S [0] default +-seq_weight S [0] t_coffee +-align FL [1] 1 +-mocca FL [0] 0 +-domain FL [0] 0 +-start D [0] 0 +-len D [0] 0 +-scale D [0] 0 +-mocca_interactive FL [0] 0 +-method_evaluate_mode S [0] default +-evaluate_mode S [0] t_coffee_fast +-get_type FL [0] 0 +-clean_aln D [0] 0 +-clean_threshold D [1] 1 +-clean_iteration D [1] 1 +-clean_evaluate_mode S [0] t_coffee_fast +-extend_matrix FL [0] 0 +-prot_min_sim D [0] 0 +-prot_max_sim D [90] 90 +-prot_min_cov D [0] 0 +-pdb_min_sim D [35] 35 +-pdb_max_sim D [100] 100 +-pdb_min_cov D [50] 50 +-pdb_blast_server W_F [0] EBI +-blast W_F [0] +-blast_server W_F [0] EBI +-pdb_db W_F [0] pdb +-protein_db W_F [0] uniprot +-method_log W_F [0] no +-struc_to_use S [0] +-cache W_F [0] use +-align_pdb_param_file W_F [0] no +-align_pdb_hasch_mode W_F [0] hasch_ca_trace_bubble +-external_aligner S [0] NO +-msa_mode S [0] tree +-one2all S [0] +-subset2all S [0] +-lalign_n_top D [0] 10 +-iterate D [0] 0 +-trim D [0] 0 +-split D [0] 0 +-trimfile S [0] default +-split D [0] 0 +-split_nseq_thres D [0] 0 +-split_score_thres D [0] 0 +-check_pdb_status D [0] 0 +-clean_seq_name D [0] 0 +-seq_to_keep S [0] +-dpa_master_aln S [0] +-dpa_maxnseq D [0] 0 +-dpa_min_score1 D [0] +-dpa_min_score2 D [0] +-dpa_keep_tmpfile FL [0] 0 +-dpa_debug D [0] 0 +-multi_core S [0] templates_jobs_relax_msa +-n_core D [1] 1 +-lib_list S [0] +-prune_lib_mode S [0] 5 +-tip S [0] one +-rna_lib S [0] +-no_warning D [0] 0 +-run_local_script D [0] 0 +-plugins S [0] default +-proxy S [0] unset +-email S [0] +-clean_overaln D [0] 0 +-overaln_param S [0] +-overaln_mode S [0] +-overaln_model S [0] +-overaln_threshold D [0] 0 +-overaln_target D [0] 0 +-overaln_P1 D [0] 0 +-overaln_P2 D [0] 0 +-overaln_P3 D [0] 0 +-overaln_P4 D [0] 0 +-exon_boundaries S [0] + +INPUT FILES + Input File (S) fasta.in Format fasta_seq + Input File (M) proba_pair + +INPUT SEQUENCES: 9 SEQUENCES [PROTEIN] + Input File fasta.in Seq Sequence0 Length 113 type PROTEIN Struct Unchecked + Input File fasta.in Seq Sequence1 Length 52 type PROTEIN Struct Unchecked + Input File fasta.in Seq Sequence2 Length 53 type PROTEIN Struct Unchecked + Input File fasta.in Seq Sequence3 Length 80 type PROTEIN Struct Unchecked + Input File fasta.in Seq Sequence4 Length 45 type PROTEIN Struct Unchecked + Input File fasta.in Seq Sequence5 Length 56 type PROTEIN Struct Unchecked + Input File fasta.in Seq Sequence6 Length 62 type PROTEIN Struct Unchecked + Input File fasta.in Seq Sequence7 Length 40 type PROTEIN Struct Unchecked + Input File fasta.in Seq Sequence8 Length 61 type PROTEIN Struct Unchecked + +COMPUTE PAIRWISE SIMILARITY [dp_mode: ] [distance_matrix_mode: ktup][Similarity Measure: idmat_sim1] + + Seq: Sequence0 + Seq: Sequence1 + Seq: Sequence2 + Seq: Sequence3 + Seq: Sequence4 + Seq: Sequence5 + Seq: Sequence6 + Seq: Sequence7 + Seq: Sequence8 + +READ/MAKE LIBRARIES:[2] + + proba_pair [method] + + [Submit Job][TOT= 36][ 0 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 5 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 8 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 11 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 13 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 16 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 19 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 22 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 25 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 27 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 30 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 33 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 36 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 38 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 41 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 44 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 47 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 50 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 52 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 55 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 58 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 61 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 63 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 66 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 69 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 72 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 75 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 77 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 80 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 83 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 86 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 88 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 91 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 94 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][ 97 %][ELAPSED TIME: 0 sec.] + [Submit Job][TOT= 36][100 %][ELAPSED TIME: 0 sec.] + +MANUAL PENALTIES: gapopen=0 gapext=0 + + Library Total Size: [6542] + +Library Relaxation:[6542] --->[5767] + + #### File Type= WEIGHT Format= tc_weight Name= no | NOT PRODUCED [WARNING:T-COFFEE:Version_8.14] + + +WEIGHTED MODE:t_coffee + + Sequence0 1.08 + Sequence1 0.82 + Sequence2 1.07 + Sequence3 1.08 + Sequence4 1.05 + Sequence5 0.82 + Sequence6 0.95 + Sequence7 1.05 + Sequence8 1.07 + + +MAKE GUIDE TREE + [MODE=nj][DONE] + +PROGRESSIVE_ALIGNMENT [Tree Based] + + Group 10: [Group 8 ( 1 seq)] with [Group 5 ( 1 seq)]-->[Score= 31][Len= 48][PID:23942] + Group 11: [Group 10 ( 2 seq)] with [Group 3 ( 1 seq)]-->[Score= 32][Len= 55][PID:23942] + Group 12: [Group 9 ( 1 seq)] with [Group 11 ( 3 seq)]-->[Score= 34][Len= 63][PID:23942] + Group 13: [Group 12 ( 4 seq)] with [Group 4 ( 1 seq)]-->[Score= 11][Len= 95][PID:23942] + Group 14: [Group 6 ( 1 seq)] with [Group 2 ( 1 seq)]-->[Score= 80][Len= 56][PID:23942] + Group 15: [Group 7 ( 1 seq)] with [Group 14 ( 2 seq)]-->[Score= 63][Len= 62][PID:23942] + Group 16: [Group 15 ( 3 seq)] with [Group 13 ( 5 seq)]-->[Score= 12][Len= 102][PID:23942] + Group 17: [Group 1 ( 1 seq)] with [Group 16 ( 8 seq)]-->[Score= 11][Len= 142][PID:23942] + + + +OUTPUT RESULTS + #### File Type= GUIDE_TREE Format= newick Name= fasta.dnd + #### File Type= MSA Format= clustalw Name= fasta.clustalw + + +# TIP :See The Full Documentation on www.tcoffee.org +# TIP 1: Get the most accurate protein alignments with: t_coffee -special_mode accurate [Slow] +# TIP 10: -usetree= to use your own guide tree + +# 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] +# T-COFFEE Memory Usage: Current= 11.932 Mb, Max= 13.916 Mb +# T-COFFEE CPU Usage: 250 millisec +# Results Produced with T-COFFEE (Version_8.14) +# T-COFFEE is available from http://www.tcoffee.org