/projects/compbio/experiments/casp5/scripts-human/create_summary_html \ T0147_twice file:/projects/compbio/experiments/casp5/t0147/t0147_twice > /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_master_table_head_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html \ Inputs >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html echo Received sequence T0147_twice.a2m Received sequence T0147_twice.a2m /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Submitted sequence(s)" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.a2m T0147_twice.a2m >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Provided documentation" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.doc.html T0147_twice.doc.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "SAM_T02 multiple alignment in a2m format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.a2m.gz T0147_twice.t2k.a2m.gz >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "SAM_T02 multiple alignment in pretty html format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.pa.html T0147_twice.t2k.pa.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "SAM_T02 target hidden Markov model" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k-w0.5.mod T0147_twice.t2k-w0.5.mod >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html \ "Secondary Structure Prediction" >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "DSSP EBGHSTL structure prediction CASP format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.dssp-ebghstl T0147_twice.t2k.dssp-ebghstl >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "DSSP EBGHSTL structure prediction RDB format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.dssp-ebghstl.rdb T0147_twice.t2k.dssp-ebghstl.rdb >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "DSSP EBGHSTL structure prediction sequence format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.dssp-ebghstl.seq T0147_twice.t2k.dssp-ebghstl.seq >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Stride EBGHTL structure prediction CASP format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.stride-ebghtl T0147_twice.t2k.stride-ebghtl >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Stride EBGHTL structure prediction RDB format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.stride-ebghtl.rdb T0147_twice.t2k.stride-ebghtl.rdb >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Stride EBGHTL structure prediction sequence format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.stride-ebghtl.seq T0147_twice.t2k.stride-ebghtl.seq >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Str structure prediction CASP format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.str T0147_twice.t2k.str >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Str structure prediction RDB format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.str.rdb T0147_twice.t2k.str.rdb >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Str structure prediction sequence format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.str.seq T0147_twice.t2k.str.seq >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Alpha angle prediction RDB format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.alpha.rdb T0147_twice.t2k.alpha.rdb >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Alpha angle prediction sequence format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.alpha.seq T0147_twice.t2k.alpha.seq >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "DSSP 3-value prediction RDB format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.dssp_ehl2.rdb T0147_twice.t2k.dssp_ehl2.rdb >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html \ "Sequence Logos" >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "SAM_T02 multiple alignment in sequence logo format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.w0.5-logo.eps T0147_twice.t2k.w0.5-logo.eps >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "DSSP EBGHSTL structure prediction in sequence logo format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.dssp-ebghstl-logo.eps T0147_twice.t2k.dssp-ebghstl-logo.eps >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Stride EBGHTL structure prediction in sequence logo format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.stride-ebghtl-logo.eps T0147_twice.t2k.stride-ebghtl-logo.eps >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Str structure prediction in sequence logo format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.str-logo.eps T0147_twice.t2k.str-logo.eps >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Alpha angle prediction in sequence logo format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.alpha-logo.eps T0147_twice.t2k.alpha-logo.eps >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "DSSP 3-value prediction in sequence logo format" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.dssp_ehl2-logo.eps T0147_twice.t2k.dssp_ehl2-logo.eps >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html \ "Target model scores" >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Annotated amino acid/100-30-dssp-ebghstl two-track target model scores" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k-100-30-dssp-ebghstl-scores.html \ T0147_twice.t2k-100-30-dssp-ebghstl-scores.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Annotated amino acid/100-30-stride-ebghtl two-track target model scores" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k-100-30-stride-ebghtl-scores.html \ T0147_twice.t2k-100-30-stride-ebghtl-scores.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Annotated amino acid/100-30-str two-track target model scores" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k-100-30-str-scores.html \ T0147_twice.t2k-100-30-str-scores.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Annotated amino acid/100-30-alpha two-track target model scores" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k-100-30-alpha-scores.html \ T0147_twice.t2k-100-30-alpha-scores.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Annotated amino acid/100-30-dssp_ehl2 two-track target model scores" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k-100-30-dssp_ehl2-scores.html \ T0147_twice.t2k-100-30-dssp_ehl2-scores.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Annotated amino acid single-track target model scores of PDB" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k-w0.5-scores.html \ T0147_twice.t2k-w0.5-scores.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html \ "Template model scores" >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Annotated template model scores" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.template-lib-scores.html \ T0147_twice.template-lib-scores.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html \ "Top Hits" >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Best scoring hits from all models" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.best-scores.html \ T0147_twice.t2k.best-scores.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html \ "Alignments for Top Hits" >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "T02 Many Alignments Summary" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.many_alignments.html\ T0147_twice.t2k.many_alignments.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "T02 Top Models Summary" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.top_reported_alignments.html\ T0147_twice.t2k.top_reported_alignments.html >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html \ "Undertaker (3d) files" >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Script for dssp coloring in rasmol" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.dssp-color.rasmol T0147_twice.t2k.dssp-color.rasmol \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Script for stride coloring in rasmol" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.stride-color.rasmol T0147_twice.t2k.stride-color.rasmol \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Script for str coloring in rasmol" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.str-color.rasmol T0147_twice.t2k.str-color.rasmol \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Script for alpha coloring in rasmol" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.alpha-color.rasmol T0147_twice.t2k.alpha-color.rasmol \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html make: *** No rule to make target `dssp_ehl2_color_script', needed by `rasmol_scripts'. /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Multiple alignment for undertaker templates" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k-2track-undertaker.a2m T0147_twice.t2k-2track-undertaker.a2m >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "many alignments for undertaker templates" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.undertaker-align.script T0147_twice.t2k.undertaker-align.script >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /cse/faculty/karplus/undertaker/undertaker < show-align.script >& show-align.log gzip -f T0147_twice.t2k.undertaker-align.pdb /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "PDB file with models for many alignments" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.undertaker-align.pdb.gz T0147_twice.t2k.undertaker-align.pdb.gz >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/bin/i686/fragfinder T0147_twice.t2k \ -a protein,STR \ -trackmod T0147_twice.t2k-w0.5.mod,T0147_twice.t2k.str.mod \ -track_coeff 1.0,0.3 \ -db /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs \ -firstsequence T0147_twice.a2m,- \ -fraglen 9 -numpermatch 6 SAM: /projects/compbio/bin/i686/fragfinder v3.3.2 (February, 2001) compiled no_date T0147_twice.t2k-w0.5.mod(5941): Reading track 0 model from MODEL -- Model from alignment file /var/tmp/tmp-build-weighted-model-bray-30427/tmp.a2m T0147_twice.t2k.str.mod(2969): Reading track 1 model from MODEL -- Model from 2nd structure file T0147_twice.t2k.str.rdb mkdir decoys /projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html \ "Fragment list for undertaker (from fragfinder)" \ file:/projects/compbio/experiments/casp5/t0147/t0147_twice/T0147_twice.t2k.frag T0147_twice.t2k.frag >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html /projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_summary_html \ >> /projects/compbio/experiments/casp5/t0147/t0147_twice/summary.html make: Target `default' not remade because of errors.