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


## SMRTlink log ----------------------------- ##

[INFO] [2020-04-07T23:16:12.166+02:00] Initial Setup of resources. Starting to run engine job id:492 type:analysis 
[INFO] [2020-04-07T23:16:12.219+02:00] Successfully validated Job Options AnalysisJobOptions(Some(Agroscope_PB33_MM_20200407 - PacBio_33-Cell2 (bc1001_BAK8A_OA--bc1001_BAK8A_OA)),None,cromwell.workflows.pb_assembly_microbial,List(BoundServiceEntryPoint(eid_subread,PacBio.DataSet.SubreadSet,IntIdAble(490))),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] [2020-04-07T23:16:12.232+02:00] Skipping Sending Email for Job 492 state:RUNNING. type:analysis userEmail:None, System is not configured for Email sending
[INFO] [2020-04-07T23:16:13.059+02:00] Final task options before converting to Cromwell inputs:
[INFO] [2020-04-07T23:16:13.139+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] [2020-04-07T23:16:13.154+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] [2020-04-07T23:16:13.154+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] [2020-04-07T23:16:13.185+02:00] Submitting Cromwell workflow to http://localhost:9096
[INFO] [2020-04-07T23:16:13.574+02:00] Started Cromwell workflow 21b82f48-b1ad-48f8-a6a6-34dcb3260e8d from SMRT Link job 677f4253-e311-416d-9af1-8be82de0f07f
[INFO] [2020-04-07T23:16:23.611+02:00] Cromwell workflow now in state Submitted
[INFO] [2020-04-07T23:16:23.652+02:00] 0 tasks finished
[INFO] [2020-04-07T23:16:33.851+02:00] Cromwell workflow now in state Running
[INFO] [2020-04-07T23:16:34.086+02:00] Created symlink to /opt/pacbio/jobs_root/cromwell-executions/pb_assembly_microbial/21b82f48-b1ad-48f8-a6a6-34dcb3260e8d
[INFO] [2020-04-07T23:16:34.231+02:00] 0 tasks finished, task pb_assembly_microbial.generate_config and 0 others running
[INFO] [2020-04-07T23:16:46.722+02:00] 1 task finished, task pb_assembly_clr.build_raw_rdb and 0 others running
[INFO] [2020-04-07T23:18:05.410+02:00] 2 tasks finished
[INFO] [2020-04-07T23:18:35.895+02:00] 3 tasks finished, task pb_assembly_clr.ovlcns_raw_run and 0 others running
[INFO] [2020-04-08T00:08:04.998+02:00] 5 tasks finished
[INFO] [2020-04-08T00:09:05.594+02:00] 6 tasks finished
[INFO] [2020-04-08T00:12:07.082+02:00] 6 tasks finished, task pb_assembly_clr.ovl_erc_prepare and 0 others running
[INFO] [2020-04-08T00:13:07.512+02:00] 7 tasks finished, task pb_assembly_clr.ovl_erc_run and 0 others running
[INFO] [2020-04-08T00:18:10.631+02:00] 8 tasks finished
[INFO] [2020-04-08T00:27:09.132+02:00] 9 tasks finished
[INFO] [2020-04-08T00:33:44.408+02:00] 11 tasks finished, task pb_assembly_microbial.create_datasets and 0 others running
[INFO] [2020-04-08T00:38:03.459+02:00] 14 tasks finished, task mapping.pbmm2_align and 0 others running
[INFO] [2020-04-08T00:43:04.113+02:00] 17 tasks finished, task mapping.pbmm2_align and 1 other running
[INFO] [2020-04-08T00:48:04.881+02:00] 23 tasks finished, task pb_assembly_clr.ovlcns_raw_run and 0 others running
[INFO] [2020-04-08T00:53:05.689+02:00] 28 tasks finished
[INFO] [2020-04-08T00:58:06.447+02:00] 36 tasks finished, task RaptorGraphMapping.graph_mapping and 1 other running
[INFO] [2020-04-08T01:03:07.273+02:00] 39 tasks finished, task RaptorGraphMapping.graph_mapping and 2 others running
[INFO] [2020-04-08T01:08:08.085+02:00] 43 tasks finished
[INFO] [2020-04-08T01:18:09.888+02:00] 44 tasks finished
[INFO] [2020-04-08T01:23:10.688+02:00] 49 tasks finished, task consensus.genomic_consensus and 0 others running
[INFO] [2020-04-08T01:28:12.546+02:00] 49 tasks finished, task consensus.genomic_consensus and 3 others running
[INFO] [2020-04-08T01:38:13.924+02:00] 50 tasks finished, task consensus.genomic_consensus and 3 others running
[INFO] [2020-04-08T02:28:19.902+02:00] 51 tasks finished, task consensus.genomic_consensus and 2 others running
[INFO] [2020-04-08T02:33:19.990+02:00] Cromwell workflow now in state Succeeded
[INFO] [2020-04-08T02:33:20.129+02:00] 61 tasks finished
[INFO] [2020-04-08T02:33:20.624+02:00] about to write datastore for job 677f4253-e311-416d-9af1-8be82de0f07f
[INFO] [2020-04-08T02:33:20.625+02:00] Done writing datastore for job 677f4253-e311-416d-9af1-8be82de0f07f
[INFO] [2020-04-08T02:33:20.625+02:00] Successfully completed running core job id:677f4253-e311-416d-9af1-8be82de0f07f
[INFO] [2020-04-08T02:33:20.711+02:00] DataStoreFile 590926fe-f7f4-4c97-89c4-704a5ed9a982 PacBio.FileTypes.log already exists. File:/opt/pacbio/smrt/userdata/jobs_root/0000/0000000/0000000492/logs/workflow.21b82f48-b1ad-48f8-a6a6-34dcb3260e8d.log
Successfully imported DSF 46ecfe42-6e7c-49a9-91e3-f0c377b5ff1c type:PacBio.FileTypes.txt
Already added report 5e70caee-f007-410b-bbde-4220321647dd (pb_assembly_microbial.report_polished_assembly) to datastore
Successfully imported DSF c3eae6dc-6659-4bac-95d8-9acca0606a39 type:PacBio.FileTypes.Fasta
Successfully imported DSF 9c8c9eb7-3544-4c14-abeb-7a5a84c0aef4 type:PacBio.FileTypes.bam
Successfully imported DSF 6d0ed98a-31f5-4fd6-bdb2-f6aa5a454554 type:PacBio.FileTypes.bam_bai
Successfully imported DSF 37471d37-41aa-4425-ba1f-abc2c57b9f94 type:PacBio.FileTypes.gff
Job id:492 DataStoreFile 430eef93-e475-e8df-9aee-4b5b9cefad72 imported
Successfully imported DSF 38951c23-f526-4c61-bdb1-c2f94a83a9fe type:PacBio.FileTypes.Fasta
Successfully imported DSF 596580f1-cb8f-4945-a545-85ee8e691863 type:PacBio.FileTypes.Fasta
Already added report 8ad94ffa-c4af-4a82-bb10-76c979f0654a (pb_assembly_microbial.report_mapping_stats) to datastore
Already added report d6728136-7da1-4cf0-b8c0-75809bc56f01 (pb_assembly_microbial.report_coverage) to datastore
Successfully imported DSF 8691bb35-2224-48f9-9f9d-4bf8e1405f55 type:PacBio.FileTypes.Fastq
Successfully imported DSF b03b4a8a-ff8f-4a0b-a073-44d2d2da3d16 type:PacBio.FileTypes.json
[INFO] [2020-04-08T02:33:20.716+02:00] Updated job 677f4253-e311-416d-9af1-8be82de0f07f state to SUCCESSFUL
[INFO] [2020-04-08T02:33:20.719+02:00] Job 492 type:analysis state:SUCCESSFUL is NOT eligible for email sending. no createdByEmail user. Skipping sending Email