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] [2020-04-07T23:10:32.151+02:00] Initial Setup of resources. Starting to run engine job id:491 type:analysis 
[INFO] [2020-04-07T23:10:32.212+02:00] Successfully validated Job Options AnalysisJobOptions(Some(Agroscope_PB33_MM_20200407 - PacBio_33-Cell2 (bc1002_BAK8A_OA--bc1002_BAK8A_OA)),None,cromwell.workflows.pb_assembly_microbial,List(BoundServiceEntryPoint(eid_subread,PacBio.DataSet.SubreadSet,IntIdAble(491))),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] [2020-04-07T23:10:32.237+02:00] Skipping Sending Email for Job 491 state:RUNNING. type:analysis userEmail:None, System is not configured for Email sending
[INFO] [2020-04-07T23:10:32.847+02:00] Final task options before converting to Cromwell inputs:
[INFO] [2020-04-07T23:10:32.848+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] [2020-04-07T23:10:32.848+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] [2020-04-07T23:10:32.848+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] [2020-04-07T23:10:32.851+02:00] Submitting Cromwell workflow to http://localhost:9096
[INFO] [2020-04-07T23:10:33.256+02:00] Started Cromwell workflow 8191f00b-9504-4f52-9653-d158d99ea0c5 from SMRT Link job 2491fedd-5a1f-4724-94e3-b255873f7ce6
[INFO] [2020-04-07T23:10:43.319+02:00] Cromwell workflow now in state Submitted
[INFO] [2020-04-07T23:10:43.510+02:00] 0 tasks finished
[INFO] [2020-04-07T23:10:53.851+02:00] Cromwell workflow now in state Running
[INFO] [2020-04-07T23:10:53.950+02:00] Created symlink to /opt/pacbio/jobs_root/cromwell-executions/pb_assembly_microbial/8191f00b-9504-4f52-9653-d158d99ea0c5
[INFO] [2020-04-07T23:11:21.269+02:00] 0 tasks finished, task pb_assembly_microbial.generate_config and 0 others running
[INFO] [2020-04-07T23:11:38.940+02:00] 1 task finished
[INFO] [2020-04-07T23:12:25.645+02:00] 1 task finished, task pb_assembly_clr.build_raw_rdb and 0 others running
[INFO] [2020-04-07T23:14:15.772+02:00] 3 tasks finished, task pb_assembly_clr.ovlcns_raw_run and 0 others running
[INFO] [2020-04-07T23:57:22.344+02:00] 4 tasks finished
[INFO] [2020-04-08T00:01:23.908+02:00] 5 tasks finished
[INFO] [2020-04-08T00:07:27.353+02:00] 7 tasks finished, task pb_assembly_clr.ovl_erc_run and 0 others running
[INFO] [2020-04-08T00:13:42.639+02:00] 8 tasks finished
[INFO] [2020-04-08T00:28:03.301+02:00] 9 tasks finished
[INFO] [2020-04-08T00:32:22.298+02:00] 10 tasks finished
[INFO] [2020-04-08T00:37:22.806+02:00] 15 tasks finished, task mapping.pbmm2_align and 0 others running
[INFO] [2020-04-08T00:42:23.572+02:00] 18 tasks finished, task mapping.pbmm2_align and 1 other running
[INFO] [2020-04-08T00:47:24.313+02:00] 24 tasks finished, task pb_assembly_clr.ovlcns_raw_run and 0 others running
[INFO] [2020-04-08T00:52:24.863+02:00] 37 tasks finished, task RaptorGraphMapping.graph_mapping and 2 others running
[INFO] [2020-04-08T00:57:25.869+02:00] 43 tasks finished, task RaptorGraphMapping.graph_mapping and 0 others running
[INFO] [2020-04-08T01:02:26.994+02:00] 45 tasks finished
[INFO] [2020-04-08T01:07:27.979+02:00] 51 tasks finished, task consensus.genomic_consensus and 3 others running
[INFO] [2020-04-08T01:17:29.713+02:00] 51 tasks finished, task consensus.genomic_consensus and 5 others running
[INFO] [2020-04-08T02:12:37.631+02:00] 55 tasks finished, task consensus.genomic_consensus and 1 other running
[INFO] [2020-04-08T02:17:38.931+02:00] 56 tasks finished, task consensus.genomic_consensus and 0 others running
[INFO] [2020-04-08T02:22:39.483+02:00] Cromwell workflow now in state Succeeded
[INFO] [2020-04-08T02:22:40.297+02:00] 64 tasks finished
[INFO] [2020-04-08T02:22:41.697+02:00] about to write datastore for job 2491fedd-5a1f-4724-94e3-b255873f7ce6
[INFO] [2020-04-08T02:22:41.698+02:00] Done writing datastore for job 2491fedd-5a1f-4724-94e3-b255873f7ce6
[INFO] [2020-04-08T02:22:41.699+02:00] Successfully completed running core job id:2491fedd-5a1f-4724-94e3-b255873f7ce6
[INFO] [2020-04-08T02:22:42.320+02:00] DataStoreFile 5fff8855-578b-48dd-8907-823e4b477252 PacBio.FileTypes.log already exists. File:/opt/pacbio/smrt/userdata/jobs_root/0000/0000000/0000000491/logs/workflow.8191f00b-9504-4f52-9653-d158d99ea0c5.log
Successfully imported DSF 5900c637-cbe2-42b3-b1f3-aa82e5643852 type:PacBio.FileTypes.txt
Already added report e13b50ca-10f2-4361-bdba-e0d158f10fee (pb_assembly_microbial.report_polished_assembly) to datastore
Successfully imported DSF b292e4fb-71f2-4c4d-8486-ca4929368f58 type:PacBio.FileTypes.Fasta
Successfully imported DSF 794a186c-6d2b-4416-8b96-aae74e19c4b2 type:PacBio.FileTypes.bam
Successfully imported DSF 1828e4a4-4b2a-4803-a66e-dcff57c29f22 type:PacBio.FileTypes.bam_bai
Successfully imported DSF 4d9475fe-60ac-49ba-a877-d6808e96226b type:PacBio.FileTypes.gff
Job id:491 DataStoreFile 656706f5-c4ae-93e1-ced8-9220d0fd027d imported
Successfully imported DSF 5d1db414-e7c3-493c-98ab-46b3e70d467b type:PacBio.FileTypes.Fasta
Successfully imported DSF f41a9b37-7b19-43ca-b3f4-d1177c6060f2 type:PacBio.FileTypes.Fasta
Already added report 6f7e7c0d-d92e-43c1-a0a4-204dee248996 (pb_assembly_microbial.report_mapping_stats) to datastore
Already added report f7c4ce04-d816-40c8-81b1-fe7e68f1cedb (pb_assembly_microbial.report_coverage) to datastore
Successfully imported DSF 9d69f345-939b-459e-be92-81f8fb7ec27b type:PacBio.FileTypes.Fastq
Successfully imported DSF 8d37f750-e7b5-4a82-8658-3acfa7fca7fd type:PacBio.FileTypes.json
[INFO] [2020-04-08T02:22:42.357+02:00] Updated job 2491fedd-5a1f-4724-94e3-b255873f7ce6 state to SUCCESSFUL
[INFO] [2020-04-08T02:22:42.359+02:00] Job 491 type:analysis state:SUCCESSFUL is NOT eligible for email sending. no createdByEmail user. Skipping sending Email