2020-07-27 19:07:20,455 - root - DEBUG - Running pipeline using kwargs: gene_prediction : True prodigal_meta : True area : [0, 100] prodigal_path : prodigal hmmer_path : hmmsearch sql_id : 21839 skip_steps : 0 cluster_dist : 20000 allow_trans_AT : True logging : process sql_overwrite : False scoring : True db_selection : ['MIBiG'] match_limit : 50 postgres : True server_run : True db_input : genome_parsing hmmersearch_path : hmmsearch project_folder : 21839 sub_project_folder : 21839 record_name : not specified record_definition : not specified record_id : 0 keep_permanent : False db_storage : custom_input : None sempi_credentials : Created with SeMPI 2.0 - genome_parsing - 266 2020-07-27 19:07:20,455 - root - INFO - File submitted: BGC0000317.gbk - genome_parsing - 272 2020-07-27 19:07:20,455 - root - INFO - Input parsing - genome_parsing - 279 2020-07-27 19:07:20,455 - pipeline_tools.file_handling - INFO - File type detection - input_parsing_initial - 40 2020-07-27 19:07:20,455 - pipeline_tools.file_handling - INFO - GBK found - input_parsing_initial - 50 2020-07-27 19:07:20,456 - pipeline_tools.file_handling - INFO - GBK found - input_parsing_initial - 50 2020-07-27 19:07:20,532 - pipeline_tools.file_handling - INFO - 1 record(s) found. Starting step-by-step parsing. - input_parsing_initial - 74 2020-07-27 19:07:20,546 - root - INFO - ************** Parsing record 0 ************** - genome_parsing - 293 2020-07-27 19:07:20,555 - root - DEBUG - Create prodigal tmp files - prodigal_parser - 24 2020-07-27 19:07:20,556 - root - DEBUG - Prodigal tmp files created - prodigal_parser - 32 2020-07-27 19:07:20,556 - root - DEBUG - Prodigal started - prodigal_parser - 45 2020-07-27 19:07:20,556 - root - INFO - Gene prediction. - prodigal_parser - 46 2020-07-27 19:07:20,556 - root - INFO - Running prodigal in anonymous "meta" mode due to user request. - prodigal_parser - 50 2020-07-27 19:07:21,200 - root - DEBUG - Prodigal stdout: ------------------------------------- PRODIGAL v2.6.2 [February, 2015] Univ of Tenn / Oak Ridge National Lab Doug Hyatt, Loren Hauser, et al. ------------------------------------- Request: Metagenomic, Phase: Training Initializing training files...done! ------------------------------------- Request: Metagenomic, Phase: Gene Finding Finding genes in sequence #1 (26881 bp)...done! - prodigal_parser - 78 2020-07-27 19:07:21,201 - root - DEBUG - Prodigal stderr: - prodigal_parser - 79 2020-07-27 19:07:21,201 - root - DEBUG - Converted prodigal output to gbk - prodigal_parser - 86 2020-07-27 19:07:21,202 - root - DEBUG - Sequence name too long, shortened to 16 letters. - prodigal_parser - 94 2020-07-27 19:07:21,215 - root - DEBUG - GBK created - prodigal_parser - 144 2020-07-27 19:07:21,216 - pipeline_tools.protein_prediction - DEBUG - Creation of protein fasta of the gbk for HMMER search - create_protein_fasta - 36 2020-07-27 19:07:21,218 - pipeline_tools.protein_prediction - INFO - Protein fasta created. - create_protein_fasta - 65 2020-07-27 19:07:21,221 - pipeline_tools.database_handling - DEBUG - Store as DB: meta_df.db - df2mysql - 122 2020-07-27 19:07:22,298 - pipeline_tools.database_handling - DEBUG - Done ! - df2mysql - 136 2020-07-27 19:07:22,307 - pipeline_tools.database_handling - DEBUG - Store as DB: pipeline_meta - df2postgres - 288 2020-07-27 19:07:22,382 - pipeline_tools.database_handling - DEBUG - Done ! - df2postgres - 297 2020-07-27 19:07:22,382 - root - INFO - Protein prediction - single_record_genome_parsing - 366 2020-07-27 19:07:22,383 - pipeline_tools.protein_prediction - DEBUG - HMM search started. - hmmer_wrapper - 98 2020-07-27 19:07:22,383 - pipeline_tools.protein_prediction - DEBUG - HMM Threshold file parsing. - hmmer_wrapper - 100 2020-07-27 19:07:22,384 - pipeline_tools.protein_prediction - DEBUG - HMM Threshold file parsed. - hmmer_wrapper - 113 2020-07-27 19:07:22,384 - pipeline_tools.protein_prediction - DEBUG - Hmmersearch started. - hmmer_wrapper - 114 2020-07-27 19:07:22,457 - root - DEBUG - Hmmersearch results for PF03033_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:22,457 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:22,457 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:22,524 - root - DEBUG - Hmmersearch results for ACP.hmm - hmmer_wrapper - 136 2020-07-27 19:07:22,524 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:22,524 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:22,590 - root - DEBUG - Hmmersearch results for PF02388_SO4_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:22,591 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:22,591 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:22,654 - root - DEBUG - Hmmersearch results for PCP.hmm - hmmer_wrapper - 136 2020-07-27 19:07:22,655 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:22,655 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:22,715 - root - DEBUG - Hmmersearch results for PF08990_5-Ring#6-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:22,715 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:22,716 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:22,792 - root - DEBUG - Hmmersearch results for KR_PKS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:22,793 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:22,793 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:22,866 - root - DEBUG - Hmmersearch results for PF01979_SO4_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:22,866 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:22,866 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:22,925 - root - DEBUG - Hmmersearch results for PF04101_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:22,926 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:22,926 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:22,992 - root - DEBUG - Hmmersearch results for PF07992_SS_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:22,992 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:22,992 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,037 - root - DEBUG - Hmmersearch results for PF00486_5-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,037 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,038 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,109 - root - DEBUG - Hmmersearch results for AT_PKS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,109 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,110 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,169 - root - DEBUG - Hmmersearch results for KSQ_PKS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,170 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,170 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,234 - root - DEBUG - Hmmersearch results for PF01678_NO2_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,234 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,234 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,334 - root - DEBUG - Hmmersearch results for ER_PKS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,335 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,335 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,454 - root - DEBUG - Hmmersearch results for PF00890_Sphingo#5-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,454 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,455 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,532 - root - DEBUG - Hmmersearch results for PF00201_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,532 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,532 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,620 - root - DEBUG - Hmmersearch results for PF00109_5-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,621 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,621 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,736 - root - DEBUG - Hmmersearch results for A_NRPS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,736 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,736 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,825 - root - DEBUG - Hmmersearch results for PF00685_SO4_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,825 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,825 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,887 - root - DEBUG - Hmmersearch results for PF13377_6-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,888 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,888 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:23,959 - root - DEBUG - Hmmersearch results for PF02275_Br_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:23,960 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:23,960 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,024 - root - DEBUG - Hmmersearch results for PF02801_6-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,024 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,024 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,092 - root - DEBUG - Hmmersearch results for PF00728_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,092 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,093 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,158 - root - DEBUG - Hmmersearch results for PF06722_N-Met#NO2_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,158 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,159 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,231 - root - DEBUG - Hmmersearch results for PF00743_6-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,231 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,231 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,296 - root - DEBUG - Hmmersearch results for PF01551_5-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,296 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,296 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,370 - root - DEBUG - Hmmersearch results for KS_PKS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,370 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,370 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,445 - root - DEBUG - Hmmersearch results for PF00999_Cl_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,446 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,446 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,512 - root - DEBUG - Hmmersearch results for PF12680_5-Ring#Sphingo_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,512 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,512 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,581 - root - DEBUG - Hmmersearch results for oMT.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,581 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,581 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,648 - root - DEBUG - Hmmersearch results for PF00908_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,649 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,649 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,723 - root - DEBUG - Hmmersearch results for PF16363_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,723 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,723 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,794 - root - DEBUG - Hmmersearch results for PF02838_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,794 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,795 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:24,890 - root - DEBUG - Hmmersearch results for PF13676_Br_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:24,890 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:24,890 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,019 - root - DEBUG - Hmmersearch results for PF16197_6-Ring#5-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,019 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,019 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,105 - root - DEBUG - Hmmersearch results for cMT.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,106 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,106 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,188 - root - DEBUG - Hmmersearch results for PF03559_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,188 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,188 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,251 - root - DEBUG - Hmmersearch results for PF00933_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,251 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,251 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,309 - root - DEBUG - Hmmersearch results for PF01915_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,310 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,310 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,371 - root - DEBUG - Hmmersearch results for PF13669_SO4_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,371 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,371 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,501 - root - DEBUG - Hmmersearch results for bACP.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,501 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,501 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,548 - root - DEBUG - Hmmersearch results for PF08421_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,549 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,549 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,597 - root - DEBUG - Hmmersearch results for PF04820_Cl_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,597 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,597 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,659 - root - DEBUG - Hmmersearch results for PF01075_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,659 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,659 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,718 - root - DEBUG - Hmmersearch results for PF13191_6-Ring_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,719 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,719 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,762 - root - DEBUG - Hmmersearch results for tAT_d.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,763 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,763 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,826 - root - DEBUG - Hmmersearch results for TE.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,826 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,826 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:25,968 - root - DEBUG - Hmmersearch results for PF04199_Cycle_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:25,968 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:25,968 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,040 - root - DEBUG - Hmmersearch results for nMT.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,040 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,040 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,086 - root - DEBUG - Hmmersearch results for PF13732_N-Met#SS_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,086 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,086 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,144 - root - DEBUG - Hmmersearch results for PF01041_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,144 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,144 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,195 - root - DEBUG - Hmmersearch results for PF03328_Cycle_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,195 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,195 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,244 - root - DEBUG - Hmmersearch results for DH_PKS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,244 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,245 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,301 - root - DEBUG - Hmmersearch results for PF00135_Cycle_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,301 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,301 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,342 - root - DEBUG - Hmmersearch results for DHt_PKS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,342 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,342 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,391 - root - DEBUG - Hmmersearch results for PF14885_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,391 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,392 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,502 - root - DEBUG - Hmmersearch results for CAL.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,502 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,502 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,565 - root - DEBUG - Hmmersearch results for E_NRPS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,565 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,565 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,626 - root - DEBUG - Hmmersearch results for C_NRPS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,627 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,627 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,691 - root - DEBUG - Hmmersearch results for DH2_PKS.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,691 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,691 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,745 - root - DEBUG - Hmmersearch results for PF01370_Glyco_PM.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,745 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,746 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,809 - root - DEBUG - Hmmersearch results for TD.hmm - hmmer_wrapper - 136 2020-07-27 19:07:26,809 - root - DEBUG - Hmmersearch stdout: - hmmer_wrapper - 137 2020-07-27 19:07:26,809 - root - DEBUG - Hmmersearch stderr: - hmmer_wrapper - 138 2020-07-27 19:07:26,809 - root - DEBUG - Hmmersearch finisehd. - hmmer_wrapper - 140 2020-07-27 19:07:26,809 - root - DEBUG - HMMER result parsing started. - protein2bio - 167 2020-07-27 19:07:26,809 - root - DEBUG - Writing locus mapping dict. - protein2bio - 175 2020-07-27 19:07:26,812 - root - DEBUG - Locus mapping dict written. - protein2bio - 187 2020-07-27 19:07:26,812 - root - DEBUG - Adding BGC_Domain to the gbk file. - protein2bio - 193 2020-07-27 19:07:26,837 - root - DEBUG - BGC_Domains added. - protein2bio - 281 2020-07-27 19:07:26,837 - root - DEBUG - Sort gbk features by start. - protein2bio - 283 2020-07-27 19:07:26,852 - root - DEBUG - HMMER result parsing finished. - protein2bio - 301 2020-07-27 19:07:26,852 - root - INFO - Gbk to dataframe conversion. - single_record_genome_parsing - 407 2020-07-27 19:07:26,852 - pipeline_tools.dataframe_curation - DEBUG - Convert the gbk to a pandas dataframe - gbk2df - 75 2020-07-27 19:07:26,859 - pipeline_tools.dataframe_curation - DEBUG - Dataframe created. - gbk2df - 109 2020-07-27 19:07:26,914 - pipeline_tools.dataframe_curation - INFO - Removing overlapping domains: - remove_overlap - 229 2020-07-27 19:07:26,915 - root - INFO - Dataframe curation. - single_record_genome_parsing - 444 2020-07-27 19:07:26,920 - pipeline_tools.dataframe_curation - DEBUG - Number of gene blocks: 2 - join_close_genes - 395 2020-07-27 19:07:26,920 - pipeline_tools.dataframe_curation - DEBUG - Add reordered domain id - add_reorder_based_on_strand - 46 2020-07-27 19:07:26,935 - pipeline_tools.dataframe_curation - DEBUG - Reordered domain id added - add_reorder_based_on_strand - 51 2020-07-27 19:07:26,935 - pipeline_tools.dataframe_curation - DEBUG - Create hmmer length dict. - combine_close_doms - 265 2020-07-27 19:07:26,950 - pipeline_tools.dataframe_curation - DEBUG - Done. - combine_close_doms - 267 2020-07-27 19:07:26,951 - pipeline_tools.dataframe_curation - DEBUG - Detect putative duplicates in the genome. - combine_close_doms - 278 2020-07-27 19:07:26,958 - pipeline_tools.dataframe_curation - DEBUG - No duplicates detected. - combine_close_doms - 296 2020-07-27 19:07:26,959 - root - INFO - Detect PKS modules. - single_record_genome_parsing - 452 2020-07-27 19:07:26,960 - pipeline_tools.module_prediction - DEBUG - Detection of PKS modules started - pks_detection - 215 2020-07-27 19:07:26,975 - pipeline_tools.module_prediction - DEBUG - Modules detected: Series([], Name: module_index, dtype: int64) - pks_detection - 225 2020-07-27 19:07:26,975 - pipeline_tools.module_prediction - DEBUG - Computing PKS details. - pks_detection - 226 2020-07-27 19:07:26,992 - pipeline_tools.module_prediction - DEBUG - PKS details computed. - pks_detection - 230 2020-07-27 19:07:26,993 - root - INFO - Detect NRPS modules. - single_record_genome_parsing - 456 2020-07-27 19:07:26,993 - pipeline_tools.module_prediction - DEBUG - Detection of NRPS modules started - nrps_detection - 498 2020-07-27 19:07:27,052 - pipeline_tools.module_prediction - DEBUG - Modules detected: block_id 1.0 2 2.0 3 Name: module_index, dtype: int64 - nrps_detection - 507 2020-07-27 19:07:27,053 - pipeline_tools.module_prediction - DEBUG - Computing NRPS details. - nrps_detection - 508 2020-07-27 19:07:27,097 - pipeline_tools.module_prediction - DEBUG - NRPS details computed. - nrps_detection - 513 2020-07-27 19:07:27,099 - pipeline_tools.module_prediction - DEBUG - Split block by TE or TD domain. - split_block_by_TE - 542 2020-07-27 19:07:27,102 - pipeline_tools.module_prediction - DEBUG - Done ! - split_block_by_TE - 560 2020-07-27 19:07:27,135 - pipeline_tools.module_prediction - DEBUG - Adjust start modules. - adjust_start_modules - 571 2020-07-27 19:07:27,138 - pipeline_tools.module_prediction - DEBUG - Done ! - adjust_start_modules - 577 2020-07-27 19:07:27,138 - pipeline_tools.cluster_prediction - DEBUG - Combine block to clusters. - combine_blocks - 46 2020-07-27 19:07:27,143 - pipeline_tools.cluster_prediction - DEBUG - Done ! - combine_blocks - 65 2020-07-27 19:07:27,295 - root - INFO - Predict specificity. - single_record_genome_parsing - 519 2020-07-27 19:07:27,296 - pipeline_tools.specificity.prediction_handler - DEBUG - Predict specificity for pks AT domain. - predict_specificity - 68 2020-07-27 19:07:27,297 - pipeline_tools.specificity.prediction_handler - DEBUG - Pks AT domains predicted. - predict_specificity - 84 2020-07-27 19:07:27,297 - pipeline_tools.specificity.prediction_handler - DEBUG - Predict specificity for nrps A domain. - predict_specificity - 86 2020-07-27 19:07:27,299 - pipeline_tools.specificity.prediction_handler - DEBUG - Load predictor. - use_predictor - 35 2020-07-27 19:07:27,840 - pipeline_tools.specificity.seq_utils - DEBUG - Align sequences with train sequences. - align_new_seq - 164 2020-07-27 19:07:28,577 - pipeline_tools.specificity.seq_utils - DEBUG - Alignment finished. - align_new_seq - 175 2020-07-27 19:07:30,874 - pipeline_tools.specificity.prediction_handler - DEBUG - Predictor loaded. - use_predictor - 42 2020-07-27 19:07:30,898 - pipeline_tools.specificity.prediction_handler - DEBUG - Nrps A domains predicted. - predict_specificity - 102 2020-07-27 19:07:30,966 - root - INFO - Create metabolites. - single_record_genome_parsing - 523 2020-07-27 19:07:30,967 - pipeline_tools.structure_prediction - DEBUG - Create substructure for PKS modules. - set_substructure_pks - 175 2020-07-27 19:07:30,971 - pipeline_tools.structure_prediction - DEBUG - Done ! - set_substructure_pks - 211 2020-07-27 19:07:30,971 - pipeline_tools.structure_prediction - DEBUG - Create substructure for NRPS modules. - set_substructure_nrps - 231 2020-07-27 19:07:30,980 - pipeline_tools.structure_prediction - DEBUG - Done. - set_substructure_nrps - 269 2020-07-27 19:07:30,981 - pipeline_tools.structure_prediction - DEBUG - Combine substructures to full structure. - combine_substruct - 311 2020-07-27 19:07:31,009 - pipeline_tools.structure_prediction - DEBUG - Done ! - combine_substruct - 329 2020-07-27 19:07:31,009 - root - INFO - Combine blocks to clusters. - single_record_genome_parsing - 531 2020-07-27 19:07:31,010 - pipeline_tools.cluster_prediction - DEBUG - Filter functional clusters. - get_functional_cluster - 206 2020-07-27 19:07:31,013 - pipeline_tools.cluster_prediction - DEBUG - Done ! - get_functional_cluster - 210 2020-07-27 19:07:31,013 - pipeline_tools.cluster_prediction - DEBUG - Extract cluster with modules. - get_functional_cluster - 241 2020-07-27 19:07:31,063 - pipeline_tools.cluster_prediction - DEBUG - Done ! - get_functional_cluster - 249 2020-07-27 19:07:31,063 - pipeline_tools.cluster_prediction - DEBUG - Extract cluster flattened. - get_functional_cluster - 282 2020-07-27 19:07:31,116 - pipeline_tools.cluster_prediction - INFO - Create scaffold figures. - create_figures_for_structures - 88 2020-07-27 19:07:31,140 - pipeline_tools.cluster_prediction - INFO - Done ! - create_figures_for_structures - 174 2020-07-27 19:07:31,141 - root - INFO - Create final Genebank record. - df2gbk - 286 2020-07-27 19:07:31,141 - root - DEBUG - Create domain df. - df2gbk - 292 2020-07-27 19:07:31,143 - root - DEBUG - Create module df. - df2gbk - 297 2020-07-27 19:07:31,157 - root - DEBUG - Create block df. - df2gbk - 299 2020-07-27 19:07:31,161 - root - DEBUG - Create cluster df. - df2gbk - 301 2020-07-27 19:07:31,164 - root - DEBUG - Create novel features. - df2gbk - 311 2020-07-27 19:07:31,173 - root - DEBUG - Add novel features. - df2gbk - 344 2020-07-27 19:07:31,181 - root - DEBUG - Sort gbk features by start. - df2gbk - 358 2020-07-27 19:07:31,181 - root - DEBUG - Write GBK. - df2gbk - 363 2020-07-27 19:07:31,188 - root - DEBUG - Create gbk for each cluster. - df2gbk - 367 2020-07-27 19:07:31,196 - root - DEBUG - Done. - df2gbk - 372 2020-07-27 19:07:32,877 - root - INFO - Search similar compounds in DB. - single_record_genome_parsing - 557 2020-07-27 19:07:32,879 - root - INFO - Fingerprint search of smiles : N[C@H](CCCC(=O)O)C(=O)Oc1c(O)c(ccc1) N[C@H](CCCC(=O)O)C(=O)N[C@H](CS)C(=O)N[C@@H](C(C)C)C(=O)O - DB_scoring_full - 1224 2020-07-27 19:07:32,943 - root - DEBUG - Done ! - DB_scoring_full - 1251 2020-07-27 19:07:32,943 - root - INFO - Fingerprint search in custom DB - DB_scoring_full - 1257 2020-07-27 19:07:32,943 - root - DEBUG - Done ! - DB_scoring_full - 1274 2020-07-27 19:07:32,943 - root - INFO - Matching of prediction to found compounds. - DB_scoring_full - 1276 2020-07-27 19:07:32,943 - root - DEBUG - Matching compound : CC[C@@]1(C)Oc2cc(c([S@](=O)C[C@@H](O)C[C@H](N)C(=O)O)cc2O)[C@@H](O)[C@H](NC)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H]1C(=O)NCC(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:32,984 - root - DEBUG - Matching compound : C[C@@H](NC(=O)[C@H](N)CCCNP(N)(=O)NS(=O)(=O)O)C(=O)N[C@H](CCCCN=C(N)N)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:32,999 - root - DEBUG - Matching compound : O=CN(O)CCC[C@@H](NC(=O)[C@H](CO)NC(=O)[C@H](CO)NC(=O)c1ccccc1O)C(=O)N1NCCC[C@@H]1C(=O)NCCC(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:33,115 - root - DEBUG - Matching compound : O=CN(O)CCC[C@@H](NC(=O)[C@H](CO)NC(=O)[C@@H]1COC(c2ccccc2O)=N1)C(=O)N1NCCC[C@@H]1C(=O)NCCC(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:33,167 - root - DEBUG - Matching compound : C=C(C)[C@@H]1NC(=O)[C@@H](NC)[C@@H](O)c2ccc(O)c(c2)O[C@](C)(CC)[C@@H](C(=O)N2CC=C[C@H]2C(=O)N/C(C(=O)N/C(=C/C(=O)O)C(=O)O)=C(\C)CC)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:33,191 - root - DEBUG - Matching compound : C[C@@H](O)[C@@H](NC(=O)[C@H](N)CCCN(O)C=O)C(=O)N(O)CCC[C@H](NC(=O)[C@H](N)CCCN(O)C=O)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:33,268 - root - DEBUG - Matching compound : CC(C)[C@@H](NC(=O)[C@H](CS)NC(=O)CCC[C@H]([NH3+])C(=O)[O-])C(=O)[O-] - substructure_match_pd - 1098 2020-07-27 19:07:33,309 - root - DEBUG - Matching compound : CC[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@H](CO)NC(=O)C[C@H](c2ccccc2)NC(=O)[C@H](CO)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:33,351 - root - DEBUG - Matching compound : CC(C)[C@H](NC(=O)[C@@H](NC(=O)[C@@H]1OC(=O)[C@H]1C(C)C)C(C)C)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:33,371 - root - DEBUG - Matching compound : CC[C@H](C)[C@@H]1C(=O)O[C@H]1C(=O)N[C@H]1C[C@H]1C[C@H](NC(=O)[C@H](C)N)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:33,390 - root - DEBUG - Matching compound : Cc1cccc(O)c1C1=N[C@H](C(=O)N[C@@H](CO)C(=O)N[C@H](CCCN(O)C=O)C(=O)N2NCCC[C@@H]2C(=O)NCCC(=O)O)CO1 - substructure_match_pd - 1098 2020-07-27 19:07:33,419 - root - DEBUG - Matching compound : CC[C@@H]1NC(=O)[C@@H]2[C@H](Cl)CCN2C(=O)[C@H](CO)NC(=O)C[C@H](c2ccccc2)NC(=O)[C@H](CO)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:33,445 - root - DEBUG - Matching compound : CC(=O)N(O)CCCC[C@H](NC(=O)CC(O)(CC(=O)N[C@@H](CCCCN(O)C(C)=O)C(=O)O)C(=O)O)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:33,493 - root - DEBUG - Matching compound : CC[C@@H](C)[C@H](NC(=O)[C@@H](NC(=O)[C@@H]1OC(=O)[C@H]1C(C)C)C(C)C)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:33,508 - root - DEBUG - Matching compound : CC[C@@H]1NC(=O)[C@@H]2[C@H](Cl)[C@H](Cl)CN2C(=O)[C@H](C)NC(=O)C[C@H](c2ccccc2)NC(=O)[C@H](CO)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:33,571 - root - DEBUG - Matching compound : C=C(C)[C@@H]1NC(=O)[C@@H](NC)[C@@H](O)c2cc(Cl)c(O)c(c2)O[C@](C)(CC)[C@@H](C(=O)N2CC=C[C@H]2C(=O)N/C(C(=O)N/C(=C/C(=O)O)C(=O)O)=C(\C)CC)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:33,629 - root - DEBUG - Matching compound : CC[C@@H]1NC(=O)[C@@H]2[C@H](Cl)[C@H](Cl)CN2C(=O)[C@H](CO)NC(=O)C[C@H](c2ccccc2)NC(=O)[C@H](CO)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:33,681 - root - DEBUG - Matching compound : CC(C)[C@@H]1NC(=O)[C@@H]2[C@H](Cl)[C@H](Cl)CN2C(=O)[C@H](CO)NC(=O)C[C@H](c2ccccc2)NC(=O)[C@H](CO)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:33,765 - root - DEBUG - Matching compound : CC[C@H](C)[C@@H]1C(=O)O[C@H]1C(=O)NCCC[C@H](NC(=O)[C@H](C)N)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:33,810 - root - DEBUG - Matching compound : C=C1NC(=O)C(CCc2ccc(OC)cc2)NC(=O)C(C(C)C)OC(=O)C(C)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:33,918 - root - DEBUG - Matching compound : C[C@@H](C(=O)NCCC(C(=O)O)C(O)(CC(=O)O)C(=O)O)N1C(=O)CC[C@@]1(O)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:33,981 - root - DEBUG - Matching compound : N[C@H](CCOc1ccc(/C(=N\O)C(=O)N[C@H]2CN([C@@H](C(=O)O)c3ccc(O)cc3)C2=O)cc1)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:34,019 - root - DEBUG - Matching compound : Cn1cc(C2=N[C@](C)(C(=O)N[C@H](C(=O)N[C@@](C)(CO)C(=O)O)[C@H]3CCCN3)CO2)c2c(O)cc(Cl)cc21 - substructure_match_pd - 1098 2020-07-27 19:07:34,058 - root - DEBUG - Matching compound : CC[C@@H](C)[C@@H](NC(=O)[C@H](O)Cc1ccc(O)cc1)C(=O)N1[C@H](C(=O)NCCCCN=C(N)N)C[C@@H]2CC[C@@H](OS(=O)(=O)O)C[C@@H]21 - substructure_match_pd - 1098 2020-07-27 19:07:34,119 - root - DEBUG - Matching compound : C=C(C)[C@@H]1NC(=O)[C@@H](N(C)C)[C@@H](O)c2cc(Cl)c(O)c(c2)O[C@](C)(CC)[C@@H](C(=O)N2CC=C[C@H]2C(=O)N/C(C(=O)N/C(=C/C(=O)O)C(=O)O)=C(\C)CC)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:34,173 - root - DEBUG - Matching compound : C[C@@H](O)[C@H](NC(=O)[C@@H](N)CC[C@]1(O)CNC1=O)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:34,205 - root - DEBUG - Matching compound : NC(N)=NCCC[C@@H](NC(=O)c1cccc(O)c1O)C(=O)N[C@@H](CO)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:34,225 - root - DEBUG - Matching compound : CNC(CO)C(=O)NC(CC(C)C)C(=O)NC(C(=O)NC(CO)C(=O)NC(C(=O)C(=O)NC(CO)C(=O)NC(Cc1ccc(O)cc1)C(=O)NC(CCCN)CC(=O)NC(C)C(=O)O)C(C)C)C(C)(C)O - substructure_match_pd - 1098 2020-07-27 19:07:34,331 - root - DEBUG - Matching compound : C[C@H](NC(=O)N[C@@H](Cc1ccccc1)C(=O)O)C(=O)N[C@H](C(=O)N/C=C1/C[C@@H](O)[C@H](n2ccc(=O)[nH]c2=O)O1)[C@H](C)N(C)C(=O)[C@@H](N)Cc1cccc(O)c1 - substructure_match_pd - 1098 2020-07-27 19:07:34,365 - root - DEBUG - Matching compound : CSCCC(NC(=O)NC(Cc1cccc(O)c1)C(=O)O)C(=O)NC(C(=O)N/C=C1\CC(O)C(N2CCC(=O)NC2=O)O1)C(C)N(C)C(=O)C(N)Cc1cccc(O)c1 - substructure_match_pd - 1098 2020-07-27 19:07:34,393 - root - DEBUG - Matching compound : CC(C)CC(NC(=O)C(O)C(O)C(N)CCCN=C(N)N)C1Cc2cccc(O)c2C(=O)O1 - substructure_match_pd - 1098 2020-07-27 19:07:34,494 - root - DEBUG - Matching compound : CC(C)CC(NC(=O)C(O)C(O)C1CCCN1)C1Cc2cccc(O)c2C(=O)O1 - substructure_match_pd - 1098 2020-07-27 19:07:34,510 - root - DEBUG - Matching compound : C[C@H](N)C(=O)N(C)[C@@H](C)[C@H](NC(=O)[C@H](C)NC(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O)C(=O)N/C=C1/C[C@@H](O)[C@H](n2ccc(=O)[nH]c2=O)O1 - substructure_match_pd - 1098 2020-07-27 19:07:34,594 - root - DEBUG - Matching compound : CO[C@H]1[C@@H](O)[C@H](N)[C@@H](O[C@H]2O[C@H](C(C)N)CC[C@H]2N)[C@H](O)[C@@H]1N(C)C(=O)CN.O=S(=O)(O)O.O=S(=O)(O)O - substructure_match_pd - 1098 2020-07-27 19:07:34,625 - root - DEBUG - Matching compound : C/C=C1/C(=O)N[C@@H](C(=O)O)[C@H](C)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N[C@@H](/C=C/C(C)=C/[C@H](C)[C@H](Cc2ccccc2)OC)[C@H](C)C(=O)N[C@@H](C(=O)O)CCC(=O)N1C - substructure_match_pd - 1098 2020-07-27 19:07:34,736 - root - DEBUG - Matching compound : CC(=O)OCC1=C(C(=O)O)N2C(=O)[C@@H](NC(=O)CCC[C@@H](N)C(=O)O)[C@H]2SC1 - substructure_match_pd - 1098 2020-07-27 19:07:34,768 - root - DEBUG - Matching compound : C=C(C)C[C@H](NC(=O)C(CO)NC(=O)CCCCC(C)C)C(=O)[C@@]1(CO)CO1 - substructure_match_pd - 1098 2020-07-27 19:07:34,804 - root - DEBUG - Matching compound : C=C1CS[C@H]([C@H](NC(=O)CCCC[C@@H](N)C(=O)O)C(=O)O)N=C1C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:34,829 - root - DEBUG - Matching compound : N/C(=N\C(=O)c1cccc(O)c1O)NCCC[C@@H](NC(=O)c1ccc(S(=O)(=O)O)c(O)c1O)C(=O)NCC(=O)N[C@H]1CCCN(O)C1=O - substructure_match_pd - 1098 2020-07-27 19:07:34,936 - root - DEBUG - Matching compound : C[C@H](N)C(=O)N[C@@H](Cc1cccc(O)c1)C(=O)N(C)[C@@H](C)[C@H](NC(=O)[C@H](C)NC(=O)N[C@@H](Cc1ccccc1)C(=O)O)C(=O)N/C=C1/C[C@@H](O)[C@H](n2ccc(=O)[nH]c2=O)O1 - substructure_match_pd - 1098 2020-07-27 19:07:34,996 - root - DEBUG - Matching compound : CC(C)C(N)C(=O)NC(C(=O)O)C(O)CC1CN2C(=O)CC2O1 - substructure_match_pd - 1098 2020-07-27 19:07:35,014 - root - DEBUG - Matching compound : C[C@H](N)C(=O)N[C@@H](Cc1cccc(O)c1)C(=O)N(C)[C@@H](C)[C@H](NC(=O)[C@H](C)NC(=O)N[C@@H](Cc1cccc(O)c1)C(=O)O)C(=O)N/C=C1/C[C@@H](O)[C@H](n2ccc(=O)[nH]c2=O)O1 - substructure_match_pd - 1098 2020-07-27 19:07:35,166 - root - DEBUG - Matching compound : C[C@H](NC(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O)C(=O)N[C@H](C(=O)N/C=C1/C[C@@H](O)[C@H](n2ccc(=O)[nH]c2=O)O1)[C@H](C)N(C)C(=O)[C@@H](N)Cc1cccc(O)c1 - substructure_match_pd - 1098 2020-07-27 19:07:35,192 - root - DEBUG - Matching compound : CC[C@]1(NC(=O)N(C)C)[C@@H](N)[C@H](Nc2cccc(C(C)=O)c2)[C@](O)(COC(=O)c2c(C)cccc2O)[C@]1(C)O - substructure_match_pd - 1098 2020-07-27 19:07:35,230 - root - DEBUG - Matching compound : CC(C)C[C@@H]1NC(=O)[C@@H](Cc2ccccc2)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@@H](CO)NC(=O)[C@H](CCCCN)NC(=O)[C@@H](Cc2ccccc2)NC1=O - substructure_match_pd - 1098 2020-07-27 19:07:35,274 - root - DEBUG - Matching compound : CSCCC(NC(=O)NC(Cc1cccc(O)c1)C(=O)O)C(=O)NC(C(=O)N/C=C1/CC(O)C(N2CCC(=O)NC2=O)O1)C(C)N(C)C(=O)C1Cc2cc(O)ccc2CN1 - substructure_match_pd - 1098 2020-07-27 19:07:35,405 - root - DEBUG - Matching compound : CC/C(C)=C1\OC(=O)[C@H](C)[C@@H](O)[C@H](Cc2cccnc2)NC(=O)[C@@H](NC(=O)c2ncccc2O)[C@@H](C)OC1=O - substructure_match_pd - 1098 2020-07-27 19:07:35,440 - root - DEBUG - Matching compound : CCCCCCCCCC(=O)N[C@H](C(=O)N[C@@H](CCN)C(=O)N[C@H](C(=O)NCC(=O)N[C@@H](CCCN(O)C(=O)C[C@H](C)O)C(=O)O)[C@H](O)C(=O)O)[C@H](O)C(=O)O - substructure_match_pd - 1098 2020-07-27 19:07:35,464 - root - DEBUG - Matching compound : C[C@H](NC(=O)N[C@@H](Cc1ccccc1)C(=O)O)C(=O)N[C@H](C(=O)N/C=C1/C[C@@H](O)[C@H](n2ccc(=O)[nH]c2=O)O1)[C@H](C)N(C)C(=O)[C@H](Cc1cccc(O)c1)NC(=O)CN - substructure_match_pd - 1098 2020-07-27 19:07:35,491 - root - DEBUG - Matching compound : CC(=O)NC(C(=O)OC(/C=C/C=C\C=C\C(=O)O)C1(C)CO1)C(C)c1ccccc1 - substructure_match_pd - 1098 2020-07-27 19:07:35,584 - root - DEBUG - Done ! - DB_scoring_full - 1342 2020-07-27 19:07:35,591 - pipeline_tools.database_handling - DEBUG - Store as DB: pm_df.db - df2mysql - 122 2020-07-27 19:07:37,076 - pipeline_tools.database_handling - DEBUG - Done ! - df2mysql - 136 2020-07-27 19:07:37,077 - pipeline_tools.database_handling - DEBUG - Store as DB: gbk_df.db - df2mysql - 122 2020-07-27 19:07:38,605 - pipeline_tools.database_handling - DEBUG - Done ! - df2mysql - 136 2020-07-27 19:07:38,607 - pipeline_tools.database_handling - DEBUG - Store as DB: cluster_df.db - df2mysql - 122 2020-07-27 19:07:39,792 - pipeline_tools.database_handling - DEBUG - Done ! - df2mysql - 136 2020-07-27 19:07:39,794 - pipeline_tools.database_handling - DEBUG - Store as DB: cluster_scoring_df.db - df2mysql - 122 2020-07-27 19:07:41,558 - pipeline_tools.database_handling - DEBUG - Done ! - df2mysql - 136 2020-07-27 19:07:41,559 - pipeline_tools.database_handling - DEBUG - Store as Zip - project2zip - 82 2020-07-27 19:07:41,691 - pipeline_tools.database_handling - DEBUG - Done ! - project2zip - 100 2020-07-27 19:07:41,692 - root - INFO - Write database. - single_record_genome_parsing - 575 2020-07-27 19:07:41,692 - pipeline_tools.database_handling - DEBUG - Store as DB: meta_df.db - df2mysql - 122 2020-07-27 19:07:43,142 - pipeline_tools.database_handling - DEBUG - Done ! - df2mysql - 136 2020-07-27 19:07:43,200 - pipeline_tools.database_handling - DEBUG - Store as DB: gbk - df2postgres - 288 2020-07-27 19:07:43,337 - pipeline_tools.database_handling - DEBUG - Done ! - df2postgres - 297 2020-07-27 19:07:43,350 - pipeline_tools.database_handling - DEBUG - Store as DB: cluster - df2postgres - 288 2020-07-27 19:07:43,483 - pipeline_tools.database_handling - DEBUG - Done ! - df2postgres - 297 2020-07-27 19:07:43,493 - pipeline_tools.database_handling - DEBUG - Store as DB: cluster_scoring - df2postgres - 288 2020-07-27 19:07:43,678 - pipeline_tools.database_handling - DEBUG - Done ! - df2postgres - 297 2020-07-27 19:07:43,679 - root - INFO - Finished ! - single_record_genome_parsing - 601 2020-07-27 19:07:43,679 - pipeline_tools.database_handling - INFO - Store dummy input table as DB: sempi_input_file - dummy_input_file - 34 2020-07-27 19:07:43,828 - pipeline_tools.database_handling - INFO - Done ! - dummy_input_file - 65 2020-07-27 19:07:43,829 - pipeline_tools.database_handling - INFO - Entry with id 21844 done ! - dummy_input_file - 67