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] [2020-04-07T17:53:42.151+02:00] Initial Setup of resources. Starting to run engine job id:483 type:analysis 
[INFO] [2020-04-07T17:53:42.181+02:00] Successfully validated Job Options AnalysisJobOptions(Some(Agroscope_PB33_MM_20200407 - PacBio_33-Cell2 (bc1020_BAK8B_OA--bc1020_BAK8B_OA)),None,cromwell.workflows.pb_assembly_microbial,List(BoundServiceEntryPoint(eid_subread,PacBio.DataSet.SubreadSet,IntIdAble(503))),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] [2020-04-07T17:53:42.187+02:00] Skipping Sending Email for Job 483 state:RUNNING. type:analysis userEmail:None, System is not configured for Email sending
[INFO] [2020-04-07T17:53:42.668+02:00] Final task options before converting to Cromwell inputs:
[INFO] [2020-04-07T17:53:42.676+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] [2020-04-07T17:53:42.676+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] [2020-04-07T17:53:42.676+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] [2020-04-07T17:53:42.684+02:00] Submitting Cromwell workflow to http://localhost:9096
[INFO] [2020-04-07T17:53:42.848+02:00] Started Cromwell workflow ea5007b2-9776-4034-921f-0028918e2307 from SMRT Link job f15a0b0c-8887-4f35-bd0b-463ddaa9f3ac
[INFO] [2020-04-07T17:53:52.946+02:00] Cromwell workflow now in state Submitted
[INFO] [2020-04-07T17:53:53.401+02:00] 0 tasks finished
[INFO] [2020-04-07T17:54:03.557+02:00] Cromwell workflow now in state Running
[INFO] [2020-04-07T17:54:03.866+02:00] Created symlink to /opt/pacbio/jobs_root/cromwell-executions/pb_assembly_microbial/ea5007b2-9776-4034-921f-0028918e2307
[INFO] [2020-04-07T17:54:03.949+02:00] 0 tasks finished, task pb_assembly_microbial.generate_config and 0 others running
[INFO] [2020-04-07T17:54:16.379+02:00] 1 task finished, task pb_assembly_clr.build_raw_rdb and 0 others running
[INFO] [2020-04-07T17:55:09.775+02:00] 2 tasks finished, task pb_assembly_clr.ovlcns_raw_prepare and 0 others running
[INFO] [2020-04-07T17:55:35.495+02:00] 3 tasks finished, task pb_assembly_clr.ovlcns_raw_run and 0 others running
[INFO] [2020-04-07T18:26:25.499+02:00] 4 tasks finished
[INFO] [2020-04-07T18:27:26.020+02:00] 5 tasks finished
[INFO] [2020-04-07T18:34:27.885+02:00] 6 tasks finished
[INFO] [2020-04-07T19:15:26.886+02:00] 7 tasks finished
[INFO] [2020-04-07T19:20:27.402+02:00] 10 tasks finished
[INFO] [2020-04-07T19:25:27.799+02:00] 15 tasks finished, task mapping.pbmm2_align and 0 others running
[INFO] [2020-04-07T19:30:28.641+02:00] 18 tasks finished, task mapping.pbmm2_align and 0 others running
[INFO] [2020-04-07T19:35:29.347+02:00] 22 tasks finished
[INFO] [2020-04-07T19:40:30.091+02:00] 25 tasks finished
[INFO] [2020-04-07T19:45:30.815+02:00] 26 tasks finished
[INFO] [2020-04-07T19:50:31.362+02:00] 30 tasks finished
[INFO] [2020-04-07T19:55:31.881+02:00] 35 tasks finished
[INFO] [2020-04-07T20:00:32.550+02:00] 38 tasks finished, task RaptorGraphMapping.graph_mapping and 2 others running
[INFO] [2020-04-07T20:05:33.320+02:00] 42 tasks finished
[INFO] [2020-04-07T20:10:34.031+02:00] 43 tasks finished, task RaptorGraphMapping.graph_mapping and 0 others running
[INFO] [2020-04-07T20:15:34.844+02:00] 44 tasks finished
[INFO] [2020-04-07T20:25:35.974+02:00] 46 tasks finished
[INFO] [2020-04-07T20:30:36.717+02:00] 49 tasks finished
[INFO] [2020-04-07T21:10:41.753+02:00] 50 tasks finished
[INFO] [2020-04-07T21:15:42.720+02:00] 51 tasks finished
[INFO] [2020-04-07T21:20:43.735+02:00] 53 tasks finished
[INFO] [2020-04-07T21:25:44.448+02:00] 53 tasks finished, task consensus.genomic_consensus and 0 others running
[INFO] [2020-04-07T21:30:45.223+02:00] 53 tasks finished, task consensus.genomic_consensus and 2 others running
[INFO] [2020-04-07T22:05:49.908+02:00] 53 tasks finished, task consensus.genomic_consensus and 4 others running
[INFO] [2020-04-07T22:15:51.726+02:00] 53 tasks finished, task consensus.genomic_consensus and 6 others running
[INFO] [2020-04-07T22:25:53.226+02:00] 56 tasks finished, task consensus.genomic_consensus and 3 others running
[INFO] [2020-04-07T23:06:01.619+02:00] 58 tasks finished, task consensus.genomic_consensus and 1 other running
[INFO] [2020-04-07T23:11:03.196+02:00] 59 tasks finished, task consensus.genomic_consensus and 0 others running
[INFO] [2020-04-07T23:16:03.499+02:00] Cromwell workflow now in state Succeeded
[INFO] [2020-04-07T23:16:04.879+02:00] 67 tasks finished
[INFO] [2020-04-07T23:16:07.143+02:00] about to write datastore for job f15a0b0c-8887-4f35-bd0b-463ddaa9f3ac
[INFO] [2020-04-07T23:16:07.144+02:00] Done writing datastore for job f15a0b0c-8887-4f35-bd0b-463ddaa9f3ac
[INFO] [2020-04-07T23:16:07.144+02:00] Successfully completed running core job id:f15a0b0c-8887-4f35-bd0b-463ddaa9f3ac
[INFO] [2020-04-07T23:16:07.784+02:00] DataStoreFile 912f990e-a839-4753-8c30-93411b521ee3 PacBio.FileTypes.log already exists. File:/opt/pacbio/smrt/userdata/jobs_root/0000/0000000/0000000483/logs/workflow.ea5007b2-9776-4034-921f-0028918e2307.log
Successfully imported DSF dabe8510-af4f-4b4e-aace-9a6afca67741 type:PacBio.FileTypes.txt
Already added report 4bbc1a57-63e2-4f8a-aba0-327538c47aad (pb_assembly_microbial.report_polished_assembly) to datastore
Successfully imported DSF f6f29a87-9eda-4365-9357-55263fd7faf9 type:PacBio.FileTypes.Fasta
Successfully imported DSF af739064-70eb-414f-a481-7d7f7e0bdf3f type:PacBio.FileTypes.bam
Successfully imported DSF 914ddc6d-1f9c-4ad4-abe6-4bbb9a4782ff type:PacBio.FileTypes.bam_bai
Successfully imported DSF 1434f87d-2ea1-46e0-a1da-917ab851ed85 type:PacBio.FileTypes.gff
Job id:483 DataStoreFile 4b398fd5-83c9-c866-bfa4-fd16fa8002f7 imported
Successfully imported DSF 2b22f5fb-1fbb-440d-9bde-5b2d480ca53c type:PacBio.FileTypes.Fasta
Successfully imported DSF 74b12b6c-63e7-4866-84d1-8df9a15389b2 type:PacBio.FileTypes.Fasta
Already added report 98eeafca-25c6-4934-bfce-195085d9c6bc (pb_assembly_microbial.report_mapping_stats) to datastore
Already added report 088162bb-ec98-441b-82a8-cf2a9dacbbaf (pb_assembly_microbial.report_coverage) to datastore
Successfully imported DSF da9001f4-1aed-4771-9277-34c5c0a6ce01 type:PacBio.FileTypes.Fastq
Successfully imported DSF 8a7653ce-ae78-4405-bf8c-be7ee84b1637 type:PacBio.FileTypes.json
[INFO] [2020-04-07T23:16:07.790+02:00] Updated job f15a0b0c-8887-4f35-bd0b-463ddaa9f3ac state to SUCCESSFUL
[INFO] [2020-04-07T23:16:07.840+02:00] Job 483 type:analysis state:SUCCESSFUL is NOT eligible for email sending. no createdByEmail user. Skipping sending Email