Data were demultiplexed in SMTRlink (auto-demux with default sttings) and assembled in SMRTlink using microbial assembly pipeline, SMRT Link Version 8.0.0.80529


## SMRT link log ----------------- ##

[INFO] [2020-04-07T17:53:12.225+02:00] Initial Setup of resources. Starting to run engine job id:481 type:analysis 
[INFO] [2020-04-07T17:53:12.241+02:00] Successfully validated Job Options AnalysisJobOptions(Some(Agroscope_PB33_MM_20200407 - PacBio_33-Cell2 (bc1022_BAK8B_OA--bc1022_BAK8B_OA)),None,cromwell.workflows.pb_assembly_microbial,List(BoundServiceEntryPoint(eid_subread,PacBio.DataSet.SubreadSet,IntIdAble(505))),List(ServiceTaskIntOption(microasm_genome_size,2700000,integer), ServiceTaskBooleanOption(consolidate_aligned_bam,false,boolean), ServiceTaskIntOption(microasm_length_cutoff,-1,integer), ServiceTaskIntOption(microasm_coverage,30,integer), ServiceTaskStrOption(microasm_advanced_options,,string)),List(ServiceTaskIntOption(cromwell.workflow_options.max_nchunks,24,integer), ServiceTaskIntOption(cromwell.workflow_options.nproc,4,integer), ServiceTaskStrOption(cromwell.workflow_options.log_level,INFO,string), ServiceTaskBooleanOption(cromwell.engine_options.read_from_cache,false,boolean), ServiceTaskStrOption(cromwell.engine_options.backend,Local,string), ServiceTaskBooleanOption(cromwell.engine_options.write_to_cache,true,boolean)),None,None,None,Some(installer.user.config.cromwell_00))
[INFO] [2020-04-07T17:53:12.271+02:00] Skipping Sending Email for Job 481 state:RUNNING. type:analysis userEmail:None, System is not configured for Email sending
[INFO] [2020-04-07T17:53:12.640+02:00] Final task options before converting to Cromwell inputs:
[INFO] [2020-04-07T17:53:12.650+02:00] [{
  "id": "microasm_genome_size",
  "value": 2700000,
  "optionTypeId": "integer"
}, {
  "id": "consolidate_aligned_bam",
  "value": false,
  "optionTypeId": "boolean"
}, {
  "id": "microasm_length_cutoff",
  "value": -1,
  "optionTypeId": "integer"
}, {
  "id": "microasm_coverage",
  "value": 30,
  "optionTypeId": "integer"
}, {
  "id": "microasm_advanced_options",
  "value": "",
  "optionTypeId": "string"
}, {
  "id": "microasm_plasmid_contig_len_max",
  "value": 300000,
  "optionTypeId": "integer"
}]
[INFO] [2020-04-07T17:53:12.651+02:00] Workflow options from job submission: List(ServiceTaskIntOption(cromwell.workflow_options.max_nchunks,24,integer), ServiceTaskIntOption(cromwell.workflow_options.nproc,4,integer), ServiceTaskStrOption(cromwell.workflow_options.log_level,INFO,string), ServiceTaskBooleanOption(cromwell.engine_options.read_from_cache,false,boolean), ServiceTaskStrOption(cromwell.engine_options.backend,Local,string), ServiceTaskBooleanOption(cromwell.engine_options.write_to_cache,true,boolean))
[INFO] [2020-04-07T17:53:12.651+02:00] Final engine options for analysis: {"read_from_cache":false,"write_to_cache":true,"backend":"Local","default_runtime_attributes":{"backend":"Local","maxRetries":1}}
[INFO] [2020-04-07T17:53:12.666+02:00] Submitting Cromwell workflow to http://localhost:9096
[INFO] [2020-04-07T17:53:12.915+02:00] Started Cromwell workflow 2a4c8058-8edf-466d-b4b9-47c7d81af26d from SMRT Link job 7d8aca58-4c85-43be-a0d5-42e20c2fe65e
[INFO] [2020-04-07T17:53:23.053+02:00] Cromwell workflow now in state Submitted
[INFO] [2020-04-07T17:53:23.315+02:00] 0 tasks finished
[INFO] [2020-04-07T17:53:45.841+02:00] Cromwell workflow now in state Running
[INFO] [2020-04-07T17:53:45.969+02:00] Created symlink to /opt/pacbio/jobs_root/cromwell-executions/pb_assembly_microbial/2a4c8058-8edf-466d-b4b9-47c7d81af26d
[INFO] [2020-04-07T17:53:46.122+02:00] 1 task finished
[INFO] [2020-04-07T17:54:01.128+02:00] 1 task finished, task pb_assembly_clr.build_raw_rdb and 0 others running
[INFO] [2020-04-07T17:54:18.812+02:00] 2 tasks finished
[INFO] [2020-04-07T17:54:40.184+02:00] 3 tasks finished, task pb_assembly_clr.ovlcns_raw_run and 0 others running
[INFO] [2020-04-07T18:21:55.401+02:00] 5 tasks finished, task pb_assembly_clr.build_erc_rdb and 0 others running
[INFO] [2020-04-07T18:22:56.157+02:00] 7 tasks finished, task pb_assembly_clr.ovl_erc_run and 0 others running
[INFO] [2020-04-07T18:24:57.171+02:00] 8 tasks finished
[INFO] [2020-04-07T18:25:57.674+02:00] 8 tasks finished, task pb_assembly_clr.ovl_erc_merge and 0 others running
[INFO] [2020-04-07T18:26:58.193+02:00] 9 tasks finished
[INFO] [2020-04-07T18:29:59.439+02:00] 9 tasks finished, task pb_assembly_clr.assemble and 0 others running
[INFO] [2020-04-07T18:31:00.315+02:00] 10 tasks finished
[INFO] [2020-04-07T19:15:03.110+02:00] 11 tasks finished
[INFO] [2020-04-07T19:20:03.678+02:00] 21 tasks finished
[INFO] [2020-04-07T19:25:04.520+02:00] 24 tasks finished
[INFO] [2020-04-07T19:30:05.138+02:00] 25 tasks finished, task pb_assembly_clr.ovlcns_raw_run and 0 others running
[INFO] [2020-04-07T19:35:06.134+02:00] 26 tasks finished, task pb_assembly_clr.ovlcns_raw_merge and 0 others running
[INFO] [2020-04-07T19:40:07.197+02:00] 38 tasks finished, task RaptorGraphMapping.graph_mapping and 1 other running
[INFO] [2020-04-07T19:45:08.016+02:00] 40 tasks finished, task RaptorGraphMapping.graph_mapping and 2 others running
[INFO] [2020-04-07T19:50:08.806+02:00] 46 tasks finished
[INFO] [2020-04-07T19:55:09.482+02:00] 49 tasks finished
[INFO] [2020-04-07T20:00:10.241+02:00] 53 tasks finished, task consensus.genomic_consensus and 0 others running
[INFO] [2020-04-07T20:05:11.197+02:00] 53 tasks finished, task consensus.genomic_consensus and 2 others running
[INFO] [2020-04-07T20:10:12.749+02:00] 54 tasks finished, task consensus.genomic_consensus and 2 others running
[INFO] [2020-04-07T20:15:13.597+02:00] 54 tasks finished, task consensus.genomic_consensus and 3 others running
[INFO] [2020-04-07T20:25:15.871+02:00] 54 tasks finished, task consensus.genomic_consensus and 5 others running
[INFO] [2020-04-07T21:10:21.273+02:00] 57 tasks finished, task consensus.genomic_consensus and 2 others running
[INFO] [2020-04-07T21:25:23.323+02:00] 58 tasks finished, task consensus.genomic_consensus and 1 other running
[INFO] [2020-04-07T21:30:24.126+02:00] 60 tasks finished
[INFO] [2020-04-07T22:05:33.090+02:00] 61 tasks finished
[INFO] [2020-04-07T22:10:34.427+02:00] 63 tasks finished
[INFO] [2020-04-07T22:15:35.830+02:00] 64 tasks finished
[INFO] [2020-04-07T22:20:37.441+02:00] 65 tasks finished
[INFO] [2020-04-07T22:25:37.840+02:00] Cromwell workflow now in state Succeeded
[INFO] [2020-04-07T22:25:38.586+02:00] 67 tasks finished
[INFO] [2020-04-07T22:25:41.369+02:00] about to write datastore for job 7d8aca58-4c85-43be-a0d5-42e20c2fe65e
[INFO] [2020-04-07T22:25:41.371+02:00] Done writing datastore for job 7d8aca58-4c85-43be-a0d5-42e20c2fe65e
[INFO] [2020-04-07T22:25:41.379+02:00] Successfully completed running core job id:7d8aca58-4c85-43be-a0d5-42e20c2fe65e
[INFO] [2020-04-07T22:25:41.981+02:00] DataStoreFile 5bfaff16-5e90-4e14-ae7f-55102c904797 PacBio.FileTypes.log already exists. File:/opt/pacbio/smrt/userdata/jobs_root/0000/0000000/0000000481/logs/workflow.2a4c8058-8edf-466d-b4b9-47c7d81af26d.log
Successfully imported DSF bc0a188d-ebe8-46ab-8f30-81261ea980de type:PacBio.FileTypes.txt
Already added report f38f7ec2-cd8f-4508-a579-a901f13a1d8b (pb_assembly_microbial.report_polished_assembly) to datastore
Successfully imported DSF 281d6e50-ce61-43c4-8b06-8bf9ba6e881b type:PacBio.FileTypes.Fasta
Successfully imported DSF 57bd3fc6-9cfd-46bb-81b7-cd1d294bdfbb type:PacBio.FileTypes.bam
Successfully imported DSF 4c11dad5-c895-4bd7-b6ac-8ab98efb1185 type:PacBio.FileTypes.bam_bai
Successfully imported DSF 01c28973-ffec-49b8-820f-49ae8ac79bd5 type:PacBio.FileTypes.gff
Job id:481 DataStoreFile 8aa52737-992c-4f3c-bd7f-30e28bc63e2c imported
Successfully imported DSF 95a2c422-8733-408d-9756-40312ceb47a5 type:PacBio.FileTypes.Fasta
Successfully imported DSF 26c4c2b6-2f9c-4aa3-bf5f-08d268cd896b type:PacBio.FileTypes.Fasta
Already added report ce026b0f-84ef-4473-8b73-32a1b0ef55dc (pb_assembly_microbial.report_mapping_stats) to datastore
Already added report 86c93b60-cb97-4373-b4cb-b69f3a70d6f0 (pb_assembly_microbial.report_coverage) to datastore
Successfully imported DSF 4380ade7-b11d-43a1-a530-656077cb7bc3 type:PacBio.FileTypes.Fastq
Successfully imported DSF 94bd9aef-1053-43fb-9276-9530728ae0a8 type:PacBio.FileTypes.json
[INFO] [2020-04-07T22:25:42.001+02:00] Updated job 7d8aca58-4c85-43be-a0d5-42e20c2fe65e state to SUCCESSFUL
[INFO] [2020-04-07T22:25:42.003+02:00] Job 481 type:analysis state:SUCCESSFUL is NOT eligible for email sending. no createdByEmail user. Skipping sending Email