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] [2020-04-07T21:29:52.106+02:00] Initial Setup of resources. Starting to run engine job id:489 type:analysis 
[INFO] [2020-04-07T21:29:52.146+02:00] Successfully validated Job Options AnalysisJobOptions(Some(Agroscope_PB33_MM_20200407 - PacBio_33-Cell2 (bc1010_BAK8A_OA--bc1010_BAK8A_OA)),None,cromwell.workflows.pb_assembly_microbial,List(BoundServiceEntryPoint(eid_subread,PacBio.DataSet.SubreadSet,IntIdAble(495))),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] [2020-04-07T21:29:52.149+02:00] Skipping Sending Email for Job 489 state:RUNNING. type:analysis userEmail:None, System is not configured for Email sending
[INFO] [2020-04-07T21:29:53.040+02:00] Final task options before converting to Cromwell inputs:
[INFO] [2020-04-07T21:29:53.057+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] [2020-04-07T21:29:53.057+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] [2020-04-07T21:29:53.057+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] [2020-04-07T21:29:53.091+02:00] Submitting Cromwell workflow to http://localhost:9096
[INFO] [2020-04-07T21:29:53.783+02:00] Started Cromwell workflow 76f9099a-817c-4fea-9a7f-ca088858052e from SMRT Link job b09a1729-b834-46b9-bc8c-1f4e204b67a1
[INFO] [2020-04-07T21:30:03.882+02:00] Cromwell workflow now in state Submitted
[INFO] [2020-04-07T21:30:04.073+02:00] 0 tasks finished
[INFO] [2020-04-07T21:30:14.255+02:00] Cromwell workflow now in state Running
[INFO] [2020-04-07T21:30:14.437+02:00] Created symlink to /opt/pacbio/jobs_root/cromwell-executions/pb_assembly_microbial/76f9099a-817c-4fea-9a7f-ca088858052e
[INFO] [2020-04-07T22:05:36.282+02:00] 1 task finished
[INFO] [2020-04-07T22:08:37.306+02:00] 1 task finished, task pb_assembly_clr.build_raw_rdb and 0 others running
[INFO] [2020-04-07T22:10:38.605+02:00] 2 tasks finished
[INFO] [2020-04-07T22:15:41.077+02:00] 2 tasks finished, task pb_assembly_clr.ovlcns_raw_prepare and 0 others running
[INFO] [2020-04-07T22:16:41.817+02:00] 3 tasks finished
[INFO] [2020-04-07T22:20:43.758+02:00] 3 tasks finished, task pb_assembly_clr.ovlcns_raw_run and 0 others running
[INFO] [2020-04-07T23:16:41.890+02:00] 7 tasks finished, task pb_assembly_clr.ovl_erc_run and 0 others running
[INFO] [2020-04-07T23:21:42.429+02:00] 15 tasks finished, task mapping.pbmm2_align and 1 other running
[INFO] [2020-04-07T23:26:42.840+02:00] 22 tasks finished, task pb_assembly_clr.build_raw_rdb and 0 others running
[INFO] [2020-04-07T23:31:43.324+02:00] 24 tasks finished, task pb_assembly_clr.ovlcns_raw_run and 0 others running
[INFO] [2020-04-07T23:36:43.896+02:00] 37 tasks finished
[INFO] [2020-04-07T23:41:44.743+02:00] 38 tasks finished, task RaptorGraphMapping.graph_mapping and 0 others running
[INFO] [2020-04-07T23:46:45.520+02:00] 40 tasks finished, task RaptorGraphMapping.graph_mapping and 0 others running
[INFO] [2020-04-07T23:51:46.502+02:00] 41 tasks finished
[INFO] [2020-04-08T00:01:47.940+02:00] 42 tasks finished, task RaptorGraphMapping.graph_mapping and 0 others running
[INFO] [2020-04-08T00:06:49.174+02:00] 44 tasks finished
[INFO] [2020-04-08T00:11:50.339+02:00] 48 tasks finished, task pb_assembly_microbial.auto_consolidate_alignments and 0 others running
[INFO] [2020-04-08T00:16:51.991+02:00] 51 tasks finished, task consensus.genomic_consensus and 0 others running
[INFO] [2020-04-08T00:21:53.202+02:00] 51 tasks finished, task consensus.genomic_consensus and 1 other running
[INFO] [2020-04-08T00:26:54.149+02:00] 51 tasks finished, task consensus.genomic_consensus and 3 others running
[INFO] [2020-04-08T00:31:54.929+02:00] 51 tasks finished, task consensus.genomic_consensus and 4 others running
[INFO] [2020-04-08T00:36:56.130+02:00] 51 tasks finished, task consensus.genomic_consensus and 6 others running
[INFO] [2020-04-08T01:07:02.620+02:00] 52 tasks finished, task consensus.genomic_consensus and 5 others running
[INFO] [2020-04-08T01:17:05.470+02:00] 54 tasks finished, task consensus.genomic_consensus and 3 others running
[INFO] [2020-04-08T01:22:06.985+02:00] 55 tasks finished, task consensus.genomic_consensus and 2 others running
[INFO] [2020-04-08T01:27:08.338+02:00] 58 tasks finished
[INFO] [2020-04-08T02:12:20.308+02:00] Cromwell workflow now in state Succeeded
[INFO] [2020-04-08T02:12:21.537+02:00] 65 tasks finished
[INFO] [2020-04-08T02:12:23.787+02:00] about to write datastore for job b09a1729-b834-46b9-bc8c-1f4e204b67a1
[INFO] [2020-04-08T02:12:23.789+02:00] Done writing datastore for job b09a1729-b834-46b9-bc8c-1f4e204b67a1
[INFO] [2020-04-08T02:12:23.789+02:00] Successfully completed running core job id:b09a1729-b834-46b9-bc8c-1f4e204b67a1
[INFO] [2020-04-08T02:12:24.336+02:00] DataStoreFile 68336b22-9572-4e51-8b1d-f0fbb885a304 PacBio.FileTypes.log already exists. File:/opt/pacbio/smrt/userdata/jobs_root/0000/0000000/0000000489/logs/workflow.76f9099a-817c-4fea-9a7f-ca088858052e.log
Successfully imported DSF d842b53f-122e-43a4-ad7c-8a38276bb577 type:PacBio.FileTypes.txt
Already added report 16be3da8-0822-4894-9dd0-2968c1af8b9f (pb_assembly_microbial.report_polished_assembly) to datastore
Successfully imported DSF 8b0992ad-7918-4513-8006-898e230d681d type:PacBio.FileTypes.Fasta
Successfully imported DSF 15ea18e6-e74c-48db-a28a-fcf2bbe35349 type:PacBio.FileTypes.bam
Successfully imported DSF 3d870d29-3eae-4f57-9ce7-01370d5da5dc type:PacBio.FileTypes.bam_bai
Successfully imported DSF dd37fb1c-e4ac-4c15-a788-3cdffb14dc4b type:PacBio.FileTypes.gff
Job id:489 DataStoreFile 172436f3-03a1-8112-1d78-6639546846db imported
Successfully imported DSF 04bdebe9-907a-43a3-b5b3-e4296bba8b20 type:PacBio.FileTypes.Fasta
Successfully imported DSF 3e29dd1c-4695-4b4a-b549-5df3f7d03b92 type:PacBio.FileTypes.Fasta
Already added report 51a7f77b-9104-4877-9f1e-2d743ef2244a (pb_assembly_microbial.report_mapping_stats) to datastore
Already added report e291f728-503c-47d6-b146-d22a026c4163 (pb_assembly_microbial.report_coverage) to datastore
Successfully imported DSF b5795d86-c27f-407b-83b6-6a2c05a1ed15 type:PacBio.FileTypes.Fastq
Successfully imported DSF abdeff17-1f61-43c8-9851-f6aca69336eb type:PacBio.FileTypes.json
[INFO] [2020-04-08T02:12:24.359+02:00] Updated job b09a1729-b834-46b9-bc8c-1f4e204b67a1 state to SUCCESSFUL
[INFO] [2020-04-08T02:12:24.360+02:00] Job 489 type:analysis state:SUCCESSFUL is NOT eligible for email sending. no createdByEmail user. Skipping sending Email