nextflow.log

Oct-10 09:48:10.629 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [wwwcache.sanger.ac.uk, 3128]
Oct-10 09:48:10.759 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [wwwcache.sanger.ac.uk, 3128]
Oct-10 09:48:10.760 [main] DEBUG nextflow.cli.Launcher - $> /nfs/users/nfs_s/ss34//nextflow -c /nfs/users/nfs_s/ss34/annot-nf/loc_we
b.config -c /www/ss34/annot-web/public/jobs/cb1584075907314fa80d0419/config run /nfs/users/nfs_s/ss34/annot-nf/annot.nf -resume --di
st_dir /www/ss34/annot-web/public/jobs/cb1584075907314fa80d0419
Oct-10 09:48:10.760 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.15.3
Oct-10 09:48:10.760 [main] INFO  nextflow.cli.CmdRun - Launching /nfs/users/nfs_s/ss34/annot-nf/annot.nf
Oct-10 09:48:10.780 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /nfs/users/nfs_s/ss34/annot-nf/nextflow.config
Oct-10 09:48:10.783 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /nfs/users/nfs_s/ss34/annot-nf/loc_web.config
Oct-10 09:48:10.783 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /www/ss34/annot-web/public/jobs/cb1584075907314fa
80d0419/config
Oct-10 09:48:10.785 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /nfs/users/nfs_s/ss34/annot-nf/nextflow.config
Oct-10 09:48:10.785 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /nfs/users/nfs_s/ss34/annot-nf/loc_web.config
Oct-10 09:48:10.785 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /www/ss34/annot-web/public/jobs/cb158407590731
4fa80d0419/config
Oct-10 09:48:11.573 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'standard'
Oct-10 09:48:12.523 [main] DEBUG nextflow.Session - Session uuid: c951b69d-c981-40d2-90c4-a253d69b8a7d
Oct-10 09:48:12.524 [main] DEBUG nextflow.Session - Executor pool size: 2
Oct-10 09:48:12.601 [main] DEBUG nextflow.cli.CmdRun -
  Version: 0.15.3 build 3063
  Modified: 26-08-2015 11:10 UTC (12:10 BST)
  System: Linux 3.13.0-43-generic
  Runtime: Groovy 2.3.11 on OpenJDK 64-Bit Server VM 1.7.0_79-b14
  Encoding: UTF-8 (UTF-8)
  Process: 24803@web-parasiteannot-01 [127.0.1.1]

Oct-10 09:48:12.656 [main] DEBUG nextflow.Session - Session start invoked
Oct-10 09:48:12.686 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
Oct-10 09:48:12.687 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Oct-10 09:48:15.142 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-10 09:48:15.336 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:15.336 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:15.353 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:15.364 [main] INFO  nextflow.executor.Executor - [warm up] executor > local
Oct-10 09:48:15.380 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'local' > capacity: 1; pollInte
rval: 3s; dumpInterval: 5m
Oct-10 09:48:15.402 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor
Oct-10 09:48:15.403 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Oct-10 09:48:15.423 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
Oct-10 09:48:15.627 [main] DEBUG nextflow.Session - >>> barrier register (process: prepare_noncontiguated_input)
Oct-10 09:48:15.640 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: pseudochr_seq -- creating a new instance
Oct-10 09:48:15.665 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: pseudochr_agp -- creating a new instance
Oct-10 09:48:15.665 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: scaffolds_seq -- creating a new instance
Oct-10 09:48:15.665 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: scaffolds_agp -- creating a new instance
Oct-10 09:48:15.665 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: contigs_seq -- creating a new instance
Oct-10 09:48:15.689 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > prepare_noncontiguated_input -- maxForks: 2
Oct-10 09:48:15.850 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:15.850 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:15.861 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:15.862 [main] DEBUG nextflow.Session - >>> barrier register (process: predict_tRNA)
Oct-10 09:48:15.863 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: trnas -- creating a new instance
Oct-10 09:48:15.893 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > predict_tRNA -- maxForks: 2
Oct-10 09:48:15.944 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:15.944 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:15.944 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:15.945 [main] DEBUG nextflow.Session - >>> barrier register (process: press_ncRNA_cms)
Oct-10 09:48:15.945 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: ncrna_cmindex -- creating a new instance
Oct-10 09:48:15.976 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > press_ncRNA_cms -- maxForks: 2
Oct-10 09:48:16.071 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.071 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.071 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.072 [main] DEBUG nextflow.Session - >>> barrier register (process: predict_ncRNA)
Oct-10 09:48:16.073 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: cmtblouts -- creating a new instance
Oct-10 09:48:16.120 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > predict_ncRNA -- maxForks: 2
Oct-10 09:48:16.167 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.167 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.167 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.168 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_ncrnas)
Oct-10 09:48:16.168 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: ncrnafile -- creating a new instance
Oct-10 09:48:16.215 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > merge_ncrnas -- maxForks: 2
Oct-10 09:48:16.253 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.253 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.253 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.265 [main] DEBUG nextflow.Session - >>> barrier register (process: exonerate_empty_hints)
Oct-10 09:48:16.266 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: exn_hints -- creating a new instance
Oct-10 09:48:16.310 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > exonerate_empty_hints -- maxForks: 2
Oct-10 09:48:16.323 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.323 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.323 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.325 [main] DEBUG nextflow.Session - >>> barrier register (process: ratt_make_ref_embl)
Oct-10 09:48:16.326 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: ref_embl -- creating a new instance
Oct-10 09:48:16.326 [Actor Thread 3] INFO  nextflow.processor.TaskDispatcher - [89/92d5fc] Submitted process > prepare_noncontiguated_input (1)
Oct-10 09:48:16.348 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > ratt_make_ref_embl -- maxForks: 2
Oct-10 09:48:16.351 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.363 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.363 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.365 [main] DEBUG nextflow.Session - >>> barrier register (process: run_ratt)
Oct-10 09:48:16.365 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: ratt_result -- creating a new instance
Oct-10 09:48:16.365 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: ratt_reports -- creating a new instance
Oct-10 09:48:16.381 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > run_ratt -- maxForks: 2
Oct-10 09:48:16.389 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.389 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.389 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.390 [main] DEBUG nextflow.Session - >>> barrier register (process: ratt_to_gff3)
Oct-10 09:48:16.390 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: ratt_gff3 -- creating a new instance
Oct-10 09:48:16.415 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > ratt_to_gff3 -- maxForks: 2
Oct-10 09:48:16.421 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.421 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.421 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.423 [main] DEBUG nextflow.Session - >>> barrier register (process: transcript_empty_hints)
Oct-10 09:48:16.423 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: trans_hints -- creating a new instance
Oct-10 09:48:16.445 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > transcript_empty_hints -- maxForks: 2
Oct-10 09:48:16.496 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.496 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.496 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.498 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_hints)
Oct-10 09:48:16.499 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: all_hints -- creating a new instance
Oct-10 09:48:16.561 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > merge_hints -- maxForks: 2
Oct-10 09:48:16.588 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.589 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.589 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.589 [main] DEBUG nextflow.Session - >>> barrier register (process: run_augustus_pseudo)
Oct-10 09:48:16.599 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: augustus_pseudo_gff3 -- creating a new instance
Oct-10 09:48:16.610 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > run_augustus_pseudo -- maxForks: 2
Oct-10 09:48:16.627 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.627 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.627 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.628 [main] DEBUG nextflow.Session - >>> barrier register (process: run_augustus_contigs)
Oct-10 09:48:16.628 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: augustus_ctg_gff3 -- creating a new instance
Oct-10 09:48:16.639 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > run_augustus_contigs -- maxForks: 2
Oct-10 09:48:16.641 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.641 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.641 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.642 [main] DEBUG nextflow.Session - >>> barrier register (process: make_empty_snap)
Oct-10 09:48:16.642 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: snap_gff3 -- creating a new instance
Oct-10 09:48:16.652 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_empty_snap -- maxForks: 2
Oct-10 09:48:16.665 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.666 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.666 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.667 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_genemodels)
Oct-10 09:48:16.667 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: merged_gff3 -- creating a new instance
Oct-10 09:48:16.679 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > merge_genemodels -- maxForks: 2
Oct-10 09:48:16.683 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.683 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.684 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.686 [main] DEBUG nextflow.Session - >>> barrier register (process: integrate_genemodels)
Oct-10 09:48:16.687 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: integrated_gff3 -- creating a new instance
Oct-10 09:48:16.698 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > integrate_genemodels -- maxForks: 2
Oct-10 09:48:16.701 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.702 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.702 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.702 [main] DEBUG nextflow.Session - >>> barrier register (process: remove_exons)
Oct-10 09:48:16.703 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: integrated_gff3_clean -- creating a new instance
Oct-10 09:48:16.712 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > remove_exons -- maxForks: 2
Oct-10 09:48:16.714 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.714 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.714 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.715 [main] DEBUG nextflow.Session - >>> barrier register (process: pseudogene_indexing)
Oct-10 09:48:16.715 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: pseudochr_last_index -- creating a new instance
Oct-10 09:48:16.732 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > pseudogene_indexing -- maxForks: 2
Oct-10 09:48:16.754 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.754 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.754 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.755 [main] DEBUG nextflow.Session - >>> barrier register (process: pseudogene_last)
Oct-10 09:48:16.755 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: pseudochr_last_out -- creating a new instance
Oct-10 09:48:16.788 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > pseudogene_last -- maxForks: 2
Oct-10 09:48:16.796 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.796 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.796 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.797 [main] DEBUG nextflow.Session - >>> barrier register (process: pseudogene_calling)
Oct-10 09:48:16.797 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: gff3_with_pseudogenes -- creating a new instance
Oct-10 09:48:16.816 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > pseudogene_calling -- maxForks: 2
Oct-10 09:48:16.825 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.825 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.826 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.826 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_structural)
Oct-10 09:48:16.826 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: genemodels_gff3 -- creating a new instance
Oct-10 09:48:16.845 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > merge_structural -- maxForks: 2
Oct-10 09:48:16.847 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.847 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.847 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.848 [main] DEBUG nextflow.Session - >>> barrier register (process: add_gap_features)
Oct-10 09:48:16.848 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: genemodels_with_gaps_gff3 -- creating a new instance
Oct-10 09:48:16.877 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > add_gap_features -- maxForks: 2
Oct-10 09:48:16.879 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.879 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.879 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.880 [main] DEBUG nextflow.Session - >>> barrier register (process: split_splice_models_at_gaps)
Oct-10 09:48:16.880 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: genemodels_with_gaps_split_gff3 -- creating a new instance
Oct-10 09:48:16.906 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > split_splice_models_at_gaps -- maxForks: 2
Oct-10 09:48:16.909 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.909 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.909 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.910 [main] DEBUG nextflow.Session - >>> barrier register (process: add_polypeptides)
Oct-10 09:48:16.911 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: genemodels_with_polypeptides_gff3 -- creating a new instance
Oct-10 09:48:16.929 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > add_polypeptides -- maxForks: 2
Oct-10 09:48:16.942 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.942 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.943 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.943 [main] DEBUG nextflow.Session - >>> barrier register (process: get_proteins_for_orthomcl)
Oct-10 09:48:16.943 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: genemodels_orthomcl_gff3 -- creating a new instance
Oct-10 09:48:16.943 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: proteins_target -- creating a new instance
Oct-10 09:48:16.962 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > get_proteins_for_orthomcl -- maxForks: 2
Oct-10 09:48:16.973 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:16.973 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:16.974 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:16.975 [main] DEBUG nextflow.Session - >>> barrier register (process: make_ref_input_for_orthomcl)
Oct-10 09:48:16.975 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: gg_file -- creating a new instance
Oct-10 09:48:16.975 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: shortname -- creating a new instance
Oct-10 09:48:16.975 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: mapped_fasta -- creating a new instance
Oct-10 09:48:16.993 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_ref_input_for_orthomcl -- maxForks: 2
Oct-10 09:48:17.003 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.003 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.003 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.003 [main] DEBUG nextflow.Session - >>> barrier register (process: make_target_input_for_orthomcl)
Oct-10 09:48:17.004 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: gg_file_ref -- creating a new instance
Oct-10 09:48:17.004 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: shortname_ref -- creating a new instance
Oct-10 09:48:17.004 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: mapped_fasta_ref -- creating a new instance
Oct-10 09:48:17.042 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_target_input_for_orthomcl -- maxForks: 2
Oct-10 09:48:17.059 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.059 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.060 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.060 [main] DEBUG nextflow.Session - >>> barrier register (process: blast_for_orthomcl_formatdb)
Oct-10 09:48:17.060 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: full_mapped_fasta_indexed -- creating a new instance
Oct-10 09:48:17.060 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: full_mapped_fasta_indexed_phr -- creating a new instance
Oct-10 09:48:17.060 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: full_mapped_fasta_indexed_psq -- creating a new instance
Oct-10 09:48:17.061 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: full_mapped_fasta_indexed_pin -- creating a new instance
Oct-10 09:48:17.079 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > blast_for_orthomcl_formatdb -- maxForks: 2
Oct-10 09:48:17.091 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.091 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.091 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.092 [main] DEBUG nextflow.Session - >>> barrier register (process: blast_for_orthomcl)
Oct-10 09:48:17.092 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: orthomcl_blastout -- creating a new instance
Oct-10 09:48:17.119 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > blast_for_orthomcl -- maxForks: 2
Oct-10 09:48:17.131 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.132 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.132 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.133 [main] DEBUG nextflow.Session - >>> barrier register (process: run_orthomcl)
Oct-10 09:48:17.133 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: orthomcl_cluster_out -- creating a new instance
Oct-10 09:48:17.165 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > run_orthomcl -- maxForks: 2
Oct-10 09:48:17.181 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.181 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.182 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.182 [main] DEBUG nextflow.Session - >>> barrier register (process: annotate_orthologs)
Oct-10 09:48:17.183 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: gff3_with_ortho_transferred -- creating a new instance
Oct-10 09:48:17.184 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: gaf_with_ortho_transferred -- creating a new instance
Oct-10 09:48:17.216 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > annotate_orthologs -- maxForks: 2
Oct-10 09:48:17.227 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.227 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.227 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.227 [main] DEBUG nextflow.Session - >>> barrier register (process: run_pfam)
Oct-10 09:48:17.228 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: pfam_output -- creating a new instance
Oct-10 09:48:17.254 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > run_pfam -- maxForks: 2
Oct-10 09:48:17.260 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.260 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.261 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.262 [main] DEBUG nextflow.Session - >>> barrier register (process: pfam_to_gff3)
Oct-10 09:48:17.262 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: pfam_gff3 -- creating a new instance
Oct-10 09:48:17.311 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > pfam_to_gff3 -- maxForks: 2
Oct-10 09:48:17.316 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.316 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.316 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.317 [main] DEBUG nextflow.Session - >>> barrier register (process: annotate_pfam)
Oct-10 09:48:17.317 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: gff3_with_pfam -- creating a new instance
Oct-10 09:48:17.318 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: gaf_with_pfam -- creating a new instance
Oct-10 09:48:17.346 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > annotate_pfam -- maxForks: 2
Oct-10 09:48:17.355 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.355 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.355 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.355 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.355 [main] DEBUG nextflow.Session - >>> barrier register (process: make_distribution_gff)
Oct-10 09:48:17.356 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: result_gff3 -- creating a new instance
Oct-10 09:48:17.356 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: result_agp -- creating a new instance
Oct-10 09:48:17.383 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_distribution_gff -- maxForks: 2
Oct-10 09:48:17.385 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.386 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.386 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.386 [main] DEBUG nextflow.Session - >>> barrier register (process: make_distribution_gaf)
Oct-10 09:48:17.387 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: result_gaf -- creating a new instance
Oct-10 09:48:17.406 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_distribution_gaf -- maxForks: 2
Oct-10 09:48:17.414 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.414 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.414 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.414 [main] DEBUG nextflow.Session - >>> barrier register (process: make_distribution_seqs)
Oct-10 09:48:17.415 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: result_seq -- creating a new instance
Oct-10 09:48:17.433 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_distribution_seqs -- maxForks: 2
Oct-10 09:48:17.454 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.455 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.455 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.455 [main] DEBUG nextflow.Session - >>> barrier register (process: make_genome_stats)
Oct-10 09:48:17.456 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: stats_output -- creating a new instance
Oct-10 09:48:17.470 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_genome_stats -- maxForks: 2
Oct-10 09:48:17.483 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.483 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.483 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.484 [main] DEBUG nextflow.Session - >>> barrier register (process: reference_compare)
Oct-10 09:48:17.484 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: tree_fasta -- creating a new instance
Oct-10 09:48:17.485 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: tree_genes -- creating a new instance
Oct-10 09:48:17.485 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: refcomp_protein_out -- creating a new instance
Oct-10 09:48:17.485 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: core_comp_circos -- creating a new instance
Oct-10 09:48:17.485 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: core_comp -- creating a new instance
Oct-10 09:48:17.510 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > reference_compare -- maxForks: 2
Oct-10 09:48:17.525 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.525 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.525 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.526 [main] DEBUG nextflow.Session - >>> barrier register (process: make_tree)
Oct-10 09:48:17.526 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: tree_out -- creating a new instance
Oct-10 09:48:17.526 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: tree_aln -- creating a new instance
Oct-10 09:48:17.544 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_tree -- maxForks: 2
Oct-10 09:48:17.560 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.560 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.561 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.561 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_gff3_for_gff3toembl)
Oct-10 09:48:17.561 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: embl_full_gff -- creating a new instance
Oct-10 09:48:17.562 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: embl_full_seq -- creating a new instance
Oct-10 09:48:17.580 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > merge_gff3_for_gff3toembl -- maxForks: 2
Oct-10 09:48:17.590 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.590 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.590 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.591 [main] DEBUG nextflow.Session - >>> barrier register (process: make_embl)
Oct-10 09:48:17.592 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: embl_out -- creating a new instance
Oct-10 09:48:17.610 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_embl -- maxForks: 2
Oct-10 09:48:17.628 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.628 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.628 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.629 [main] DEBUG nextflow.Session - >>> barrier register (process: make_report)
Oct-10 09:48:17.629 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: report_output -- creating a new instance
Oct-10 09:48:17.658 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_report -- maxForks: 2
Oct-10 09:48:17.660 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.661 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.661 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.661 [main] DEBUG nextflow.Session - >>> barrier register (process: make_genelist)
Oct-10 09:48:17.662 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: genelist_csv_out -- creating a new instance
Oct-10 09:48:17.684 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > make_genelist -- maxForks: 2
Oct-10 09:48:17.687 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
Oct-10 09:48:17.687 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Oct-10 09:48:17.687 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Oct-10 09:48:17.688 [main] DEBUG nextflow.Session - >>> barrier register (process: add_products_to_protein_fasta)
Oct-10 09:48:17.688 [main] DEBUG nextflow.script.BaseParam - output > channel unknown: result_protein -- creating a new instance
Oct-10 09:48:17.707 [main] DEBUG n.processor.ParallelTaskProcessor - Creating operator > add_products_to_protein_fasta -- maxForks: 2
Oct-10 09:48:17.726 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Oct-10 09:48:17.727 [main] DEBUG nextflow.Session - Session await
Oct-10 09:48:20.507 [Actor Thread 4] INFO  nextflow.processor.TaskDispatcher - [e1/6a0776] Submitted process > press_ncRNA_cms (1)
Oct-10 09:48:20.547 [Actor Thread 10] DEBUG n.splitter.AbstractTextSplitter - Splitter `splitFasta` collector path: /www/ss34/work/cb1584075907314fa80d0419/b5/22652443179a8fce506fb54a5a49b5/pseudo.pseudochr.fasta
Oct-10 09:48:20.557 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <prepare_noncontiguated_input> Sending poison pills and terminating process
Oct-10 09:48:20.570 [Actor Thread 2] DEBUG nextflow.Session - <<< barrier arrive (process: prepare_noncontiguated_input)
Oct-10 09:48:20.571 [Actor Thread 9] DEBUG n.processor.ParallelTaskProcessor - <prepare_noncontiguated_input> After stop
Oct-10 09:48:20.588 [Actor Thread 14] DEBUG n.processor.ParallelTaskProcessor - <run_augustus_contigs> Poison pill arrived
Oct-10 09:48:20.590 [Actor Thread 14] DEBUG n.processor.ParallelTaskProcessor - <run_augustus_contigs> Poison pill arrived
Oct-10 09:48:20.590 [Actor Thread 14] DEBUG n.processor.ParallelTaskProcessor - <run_augustus_contigs> Poison pill arrived
Oct-10 09:48:20.591 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <run_augustus_contigs> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.591 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <run_augustus_contigs> State before poison: StateObj[submitted: 1; completed: 0; poisoned: true; allScalar: false]
Oct-10 09:48:20.591 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <run_augustus_contigs> State before poison: StateObj[submitted: 1; completed: 0; poisoned: true; allScalar: false]
Oct-10 09:48:20.592 [Actor Thread 14] DEBUG n.processor.ParallelTaskProcessor - <run_augustus_contigs> Poison pill arrived
Oct-10 09:48:20.603 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <run_augustus_contigs> State before poison: StateObj[submitted: 1; completed: 0; poisoned: true; allScalar: false]
Oct-10 09:48:20.612 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <predict_tRNA> Poison pill arrived
Oct-10 09:48:20.612 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <run_augustus_contigs> Poison pill arrived
Oct-10 09:48:20.612 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <run_augustus_contigs> State before poison: StateObj[submitted: 1; completed: 0; poisoned: true; allScalar: false]
Oct-10 09:48:20.612 [Actor Thread 11] DEBUG n.splitter.AbstractTextSplitter - Splitter `splitFasta` collector path: /www/ss34/work/cb1584075907314fa80d0419/b5/22652443179a8fce506fb54a5a49b5/pseudo.pseudochr.fasta
Oct-10 09:48:20.622 [Actor Thread 20] DEBUG nextflow.processor.StateObj - <predict_tRNA> State before poison: StateObj[submitted: 1; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.665 [Actor Thread 9] ERROR nextflow.processor.TaskProcessor - Error executing process > 'make_distribution_seqs'

Caused by:
  Cannot obtain the semaphore to fork operator's body.

java.lang.IllegalStateException: Cannot obtain the semaphore to fork operator's body.
        at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor.startTask(ForkingDataflowOperatorActor.java:52) ~[gpars-1.2.1.jar:1.2.1]
        at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108) ~[gpars-1.2.1.jar:1.2.1]
        at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43) ~[gpars-1.2.1.jar:1.2.1]
        at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293) ~[gpars-1.2.1.jar:1.2.1]
        at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30) ~[gpars-1.2.1.jar:1.2.1]
        at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93) ~[gpars-1.2.1.jar:1.2.1]
        at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132) ~[gpars-1.2.1.jar:1.2.1]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) ~[na:1.7.0_79]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) ~[na:1.7.0_79]
        at java.lang.Thread.run(Thread.java:745) ~[na:1.7.0_79]
Caused by: java.lang.InterruptedException: null
        at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireSharedInterruptibly(AbstractQueuedSynchronizer.java:1301) ~[na:1.7.0_79]
        at java.util.concurrent.Semaphore.acquire(Semaphore.java:317) ~[na:1.7.0_79]
        at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor.startTask(ForkingDataflowOperatorActor.java:50) ~[gpars-1.2.1.jar:1.2.1]
        ... 9 common frames omitted
Oct-10 09:48:20.687 [Actor Thread 9] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.IllegalStateException: Cannot obtain the semaphore to fork operator's body.
Oct-10 09:48:20.715 [Thread-2] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
Oct-10 09:48:20.719 [main] DEBUG nextflow.Session - Session await > processes completed
Oct-10 09:48:20.720 [main] DEBUG nextflow.Session - Session await > done
Oct-10 09:48:20.774 [Actor Thread 21] DEBUG n.processor.ParallelTaskProcessor - <press_ncRNA_cms> After stop
Oct-10 09:48:20.774 [Actor Thread 17] DEBUG n.processor.ParallelTaskProcessor - <predict_tRNA> After stop
Oct-10 09:48:20.774 [Actor Thread 17] DEBUG n.processor.ParallelTaskProcessor - <predict_ncRNA> After stop
Oct-10 09:48:20.775 [main] WARN  n.processor.TaskPollingMonitor - Killing pending processes (1)
Oct-10 09:48:20.777 [Actor Thread 17] DEBUG n.processor.ParallelTaskProcessor - <merge_ncrnas> Poison pill arrived
Oct-10 09:48:20.777 [Actor Thread 20] DEBUG nextflow.processor.StateObj - <merge_ncrnas> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.777 [Actor Thread 17] DEBUG n.processor.ParallelTaskProcessor - <merge_ncrnas> After stop
Oct-10 09:48:20.777 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <exonerate_empty_hints> After stop
Oct-10 09:48:20.777 [Actor Thread 20] DEBUG nextflow.processor.TaskProcessor - <merge_ncrnas> Sending poison pills and terminating process
Oct-10 09:48:20.777 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <run_ratt> After stop
Oct-10 09:48:20.777 [Actor Thread 20] DEBUG nextflow.Session - <<< barrier arrive (process: merge_ncrnas)
Oct-10 09:48:20.777 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <ratt_to_gff3> After stop
Oct-10 09:48:20.778 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <ratt_make_ref_embl> After stop
Oct-10 09:48:20.778 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <merge_structural> Poison pill arrived
Oct-10 09:48:20.778 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <transcript_empty_hints> After stop
Oct-10 09:48:20.778 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <merge_structural> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.778 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - <merge_structural> Sending poison pills and terminating process
Oct-10 09:48:20.778 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: merge_structural)
Oct-10 09:48:20.778 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <merge_structural> After stop
Oct-10 09:48:20.779 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <merge_hints> After stop
Oct-10 09:48:20.779 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <add_gap_features> Poison pill arrived
Oct-10 09:48:20.779 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <add_gap_features> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.779 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - <add_gap_features> Sending poison pills and terminating process
Oct-10 09:48:20.779 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: add_gap_features)
Oct-10 09:48:20.780 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <add_gap_features> After stop
Oct-10 09:48:20.780 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <run_augustus_pseudo> After stop
Oct-10 09:48:20.780 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <split_splice_models_at_gaps> Poison pill arrived
Oct-10 09:48:20.780 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <split_splice_models_at_gaps> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.780 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <split_splice_models_at_gaps> Sending poison pills and terminating process
Oct-10 09:48:20.781 [Actor Thread 2] DEBUG nextflow.Session - <<< barrier arrive (process: split_splice_models_at_gaps)
Oct-10 09:48:20.781 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <run_augustus_contigs> After stop
Oct-10 09:48:20.781 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <split_splice_models_at_gaps> After stop
Oct-10 09:48:20.781 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <add_polypeptides> Poison pill arrived
Oct-10 09:48:20.781 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <add_polypeptides> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.781 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - <add_polypeptides> Sending poison pills and terminating process
Oct-10 09:48:20.782 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: add_polypeptides)
Oct-10 09:48:20.782 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <make_empty_snap> After stop
Oct-10 09:48:20.782 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <add_polypeptides> After stop
Oct-10 09:48:20.782 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <annotate_orthologs> Poison pill arrived
Oct-10 09:48:20.782 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <get_proteins_for_orthomcl> Poison pill arrived
Oct-10 09:48:20.782 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <get_proteins_for_orthomcl> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.782 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <annotate_orthologs> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.783 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <get_proteins_for_orthomcl> Sending poison pills and terminating process
Oct-10 09:48:20.783 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - <annotate_orthologs> Sending poison pills and terminating process
Oct-10 09:48:20.783 [Actor Thread 2] DEBUG nextflow.Session - <<< barrier arrive (process: get_proteins_for_orthomcl)
Oct-10 09:48:20.783 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: annotate_orthologs)
Oct-10 09:48:20.783 [Actor Thread 14] DEBUG n.processor.ParallelTaskProcessor - <annotate_orthologs> After stop
Oct-10 09:48:20.783 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <make_target_input_for_orthomcl> Poison pill arrived
Oct-10 09:48:20.783 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <get_proteins_for_orthomcl> After stop
Oct-10 09:48:20.783 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <make_target_input_for_orthomcl> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.783 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <annotate_pfam> Poison pill arrived
Oct-10 09:48:20.783 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <make_target_input_for_orthomcl> Sending poison pills and terminating process
Oct-10 09:48:20.784 [main] DEBUG n.processor.TaskPollingMonitor - Killing process (1): TaskHandler[id: 2; name: press_ncRNA_cms (1); status: RUNNING; exit: -; workDir: /www/ss34/work/cb1584075907314fa80d0419/e1/6a0776e4623bccb67087ed7ec77b19]
Oct-10 09:48:20.784 [Actor Thread 2] DEBUG nextflow.Session - <<< barrier arrive (process: make_target_input_for_orthomcl)
Oct-10 09:48:20.793 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <integrate_genemodels> After stop
Oct-10 09:48:20.793 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <remove_exons> After stop
Oct-10 09:48:20.794 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <pseudogene_indexing> After stop
Oct-10 09:48:20.794 [Actor Thread 22] DEBUG n.processor.ParallelTaskProcessor - <merge_genemodels> After stop
Oct-10 09:48:20.803 [Actor Thread 25] DEBUG n.processor.ParallelTaskProcessor - <make_target_input_for_orthomcl> After stop
Oct-10 09:48:20.803 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <annotate_pfam> Poison pill arrived
Oct-10 09:48:20.803 [Actor Thread 24] DEBUG nextflow.processor.StateObj - <annotate_pfam> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.807 [Actor Thread 14] DEBUG n.processor.ParallelTaskProcessor - <add_products_to_protein_fasta> Poison pill arrived
Oct-10 09:48:20.808 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <reference_compare> Poison pill arrived
Oct-10 09:48:20.808 [Actor Thread 21] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: /tmp/cb1584075907314fa80d0419/nxf1924589865751912494
Oct-10 09:48:20.808 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <run_pfam> Poison pill arrived
Oct-10 09:48:20.810 [Actor Thread 24] DEBUG nextflow.processor.TaskProcessor - <annotate_pfam> Sending poison pills and terminating process
Oct-10 09:48:20.811 [Actor Thread 20] DEBUG nextflow.processor.StateObj - <add_products_to_protein_fasta> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.814 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <reference_compare> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.814 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <pseudogene_last> After stop
Oct-10 09:48:20.815 [Actor Thread 14] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: /tmp/cb1584075907314fa80d0419/nxf4437385720648268451
Oct-10 09:48:20.815 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <pseudogene_calling> Poison pill arrived
Oct-10 09:48:20.823 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <run_pfam> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.823 [Actor Thread 20] DEBUG nextflow.processor.TaskProcessor - <add_products_to_protein_fasta> Sending poison pills and terminating process
Oct-10 09:48:20.823 [Actor Thread 24] DEBUG nextflow.Session - <<< barrier arrive (process: annotate_pfam)
Oct-10 09:48:20.823 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <make_distribution_gaf> Poison pill arrived
Oct-10 09:48:20.823 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <make_distribution_gff> Poison pill arrived
Oct-10 09:48:20.823 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <reference_compare> Sending poison pills and terminating process
Oct-10 09:48:20.826 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - <run_pfam> Sending poison pills and terminating process
Oct-10 09:48:20.826 [Actor Thread 20] DEBUG nextflow.Session - <<< barrier arrive (process: add_products_to_protein_fasta)
Oct-10 09:48:20.826 [Actor Thread 25] DEBUG n.processor.ParallelTaskProcessor - <annotate_pfam> After stop
Oct-10 09:48:20.826 [Actor Thread 21] DEBUG n.processor.ParallelTaskProcessor - <make_tree> Poison pill arrived
Oct-10 09:48:20.827 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: run_pfam)
Oct-10 09:48:20.827 [Actor Thread 17] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: /tmp/cb1584075907314fa80d0419/nxf1097798005802690848
Oct-10 09:48:20.827 [Actor Thread 22] DEBUG n.processor.ParallelTaskProcessor - <pfam_to_gff3> Poison pill arrived
Oct-10 09:48:20.827 [Actor Thread 25] DEBUG n.processor.ParallelTaskProcessor - <run_pfam> After stop
Oct-10 09:48:20.828 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <pfam_to_gff3> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.828 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - <pfam_to_gff3> Sending poison pills and terminating process
Oct-10 09:48:20.828 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: pfam_to_gff3)
Oct-10 09:48:20.828 [Actor Thread 17] DEBUG n.processor.ParallelTaskProcessor - <pfam_to_gff3> After stop
Oct-10 09:48:20.831 [Actor Thread 26] DEBUG nextflow.processor.StateObj - <pseudogene_calling> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.832 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - <pseudogene_calling> Sending poison pills and terminating process
Oct-10 09:48:20.832 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: pseudogene_calling)
Oct-10 09:48:20.835 [Actor Thread 2] DEBUG nextflow.Session - <<< barrier arrive (process: reference_compare)
Oct-10 09:48:20.835 [Actor Thread 24] DEBUG nextflow.processor.StateObj - <annotate_pfam> State before poison: StateObj[submitted: 0; completed: 0; poisoned: true; allScalar: false]
Oct-10 09:48:20.835 [Actor Thread 21] DEBUG n.processor.ParallelTaskProcessor - <reference_compare> After stop
Oct-10 09:48:20.836 [Actor Thread 30] DEBUG nextflow.processor.StateObj - <make_tree> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.836 [Actor Thread 30] DEBUG nextflow.processor.TaskProcessor - <make_tree> Sending poison pills and terminating process
Oct-10 09:48:20.839 [Actor Thread 30] DEBUG nextflow.Session - <<< barrier arrive (process: make_tree)
Oct-10 09:48:20.839 [Actor Thread 23] DEBUG n.processor.ParallelTaskProcessor - <make_tree> After stop
Oct-10 09:48:20.843 [Actor Thread 28] DEBUG nextflow.processor.StateObj - <make_distribution_gff> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.844 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - <make_distribution_gff> Sending poison pills and terminating process
Oct-10 09:48:20.844 [Actor Thread 23] DEBUG n.processor.ParallelTaskProcessor - <make_genome_stats> Poison pill arrived
Oct-10 09:48:20.844 [Actor Thread 17] DEBUG n.processor.ParallelTaskProcessor - <merge_gff3_for_gff3toembl> Poison pill arrived
Oct-10 09:48:20.844 [Actor Thread 21] DEBUG n.processor.ParallelTaskProcessor - <make_report> Poison pill arrived
Oct-10 09:48:20.844 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <make_genome_stats> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.845 [Actor Thread 22] DEBUG n.processor.ParallelTaskProcessor - <make_genelist> Poison pill arrived
Oct-10 09:48:20.845 [Actor Thread 24] DEBUG nextflow.processor.StateObj - <merge_gff3_for_gff3toembl> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.845 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <make_report> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.845 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <make_genome_stats> Sending poison pills and terminating process
Oct-10 09:48:20.845 [Actor Thread 24] DEBUG nextflow.processor.TaskProcessor - <merge_gff3_for_gff3toembl> Sending poison pills and terminating process
Oct-10 09:48:20.845 [Actor Thread 28] DEBUG nextflow.Session - <<< barrier arrive (process: make_distribution_gff)
Oct-10 09:48:20.845 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - <make_report> Sending poison pills and terminating process
Oct-10 09:48:20.853 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <pseudogene_calling> After stop
Oct-10 09:48:20.856 [Actor Thread 27] DEBUG nextflow.processor.StateObj - <make_distribution_gaf> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.856 [Actor Thread 2] DEBUG nextflow.Session - <<< barrier arrive (process: make_genome_stats)
Oct-10 09:48:20.859 [Actor Thread 31] DEBUG nextflow.processor.StateObj - <make_genelist> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.876 [Actor Thread 24] DEBUG nextflow.Session - <<< barrier arrive (process: merge_gff3_for_gff3toembl)
Oct-10 09:48:20.876 [Actor Thread 22] DEBUG n.processor.ParallelTaskProcessor - <make_embl> Poison pill arrived
Oct-10 09:48:20.876 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: make_report)
Oct-10 09:48:20.876 [Actor Thread 19] DEBUG n.processor.ParallelTaskProcessor - <make_distribution_gff> After stop
Oct-10 09:48:20.876 [Actor Thread 27] DEBUG nextflow.processor.TaskProcessor - <make_distribution_gaf> Sending poison pills and terminating process
Oct-10 09:48:20.876 [Actor Thread 14] DEBUG n.processor.ParallelTaskProcessor - <make_genome_stats> After stop
Oct-10 09:48:20.877 [Actor Thread 31] DEBUG nextflow.processor.TaskProcessor - <make_genelist> Sending poison pills and terminating process
Oct-10 09:48:20.877 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <make_ref_input_for_orthomcl> After stop
Oct-10 09:48:20.881 [Actor Thread 4] DEBUG n.processor.ParallelTaskProcessor - <merge_gff3_for_gff3toembl> After stop
Oct-10 09:48:20.882 [Actor Thread 29] DEBUG n.processor.ParallelTaskProcessor - <add_products_to_protein_fasta> After stop
Oct-10 09:48:20.882 [Actor Thread 22] DEBUG n.processor.ParallelTaskProcessor - <make_embl> Poison pill arrived
Oct-10 09:48:20.882 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <make_embl> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.882 [Actor Thread 25] DEBUG n.processor.ParallelTaskProcessor - <make_report> After stop
Oct-10 09:48:20.882 [Actor Thread 27] DEBUG nextflow.Session - <<< barrier arrive (process: make_distribution_gaf)
Oct-10 09:48:20.883 [Actor Thread 15] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: /tmp/cb1584075907314fa80d0419/nxf5138628417852586633
Oct-10 09:48:20.883 [Actor Thread 31] DEBUG nextflow.Session - <<< barrier arrive (process: make_genelist)
Oct-10 09:48:20.884 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - <make_embl> Sending poison pills and terminating process
Oct-10 09:48:20.884 [Actor Thread 25] DEBUG n.processor.ParallelTaskProcessor - <make_distribution_gaf> After stop
Oct-10 09:48:20.885 [Actor Thread 2] DEBUG nextflow.Session - <<< barrier arrive (process: make_embl)
Oct-10 09:48:20.885 [Actor Thread 22] DEBUG n.processor.ParallelTaskProcessor - <make_genelist> After stop
Oct-10 09:48:20.885 [Actor Thread 15] DEBUG n.processor.ParallelTaskProcessor - <make_embl> After stop
Oct-10 09:48:20.885 [Actor Thread 2] DEBUG nextflow.processor.StateObj - <make_embl> State before poison: StateObj[submitted: 0; completed: 0; poisoned: true; allScalar: false]
Oct-10 09:48:20.888 [main] DEBUG nextflow.Session - Session destroyed
Oct-10 09:48:20.892 [Actor Thread 14] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: /tmp/cb1584075907314fa80d0419/nxf4486784429682913125
Oct-10 09:48:20.892 [Actor Thread 29] DEBUG n.processor.ParallelTaskProcessor - <run_orthomcl> Poison pill arrived
Oct-10 09:48:20.893 [Actor Thread 18] DEBUG nextflow.processor.StateObj - <run_orthomcl> State before poison: StateObj[submitted: 0; completed: 0; poisoned: false; allScalar: false]
Oct-10 09:48:20.893 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - <run_orthomcl> Sending poison pills and terminating process
Oct-10 09:48:20.893 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: run_orthomcl)
Oct-10 09:48:20.893 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <run_orthomcl> After stop
Oct-10 09:48:20.894 [Actor Thread 4] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: /tmp/cb1584075907314fa80d0419/nxf5346971146158574192
Oct-10 09:48:20.895 [Actor Thread 13] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: /tmp/cb1584075907314fa80d0419/nxf6508034739742504231
Oct-10 09:48:20.895 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <blast_for_orthomcl_formatdb> After stop
Oct-10 09:48:20.895 [Actor Thread 13] DEBUG n.processor.ParallelTaskProcessor - <blast_for_orthomcl> After stop
Oct-10 09:48:20.896 [Actor Thread 4] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: /tmp/cb1584075907314fa80d0419/nxf3990597642110981887
Oct-10 09:48:20.897 [Actor Thread 29] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: /tmp/cb1584075907314fa80d0419/nxf5474322325301920102
Oct-10 09:48:20.903 [Actor Thread 9] DEBUG n.processor.ParallelTaskProcessor - <make_distribution_seqs> After stop