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  1. ```sbatch --mem=8g --partition=broadwl run_atac.sh```
  2.  
  3. ```
  4. [2018-09-21 20:02:15,33] [info] Running with database db.url = jdbc:hsqldb:mem:d3447b12-159a-4e42-84ed-95008b9b4607;shutdown=false;hsqldb.tx=mvcc
  5. [2018-09-21 20:02:35,30] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
  6. [2018-09-21 20:02:35,33] [info] [RenameWorkflowOptionsInMetadata] 100%
  7. [2018-09-21 20:02:35,80] [info] Running with database db.url = jdbc:hsqldb:mem:f9c12bea-bc1b-4b04-9c39-4a44d4e12b5b;shutdown=false;hsqldb.tx=mvcc
  8. [2018-09-21 20:02:36,59] [ESC[38;5;220mwarnESC[0m] This actor factory is deprecated. Please use cromwell.backend.google.pipelines.v1alpha2.PipelinesApiLifecycleActorFactory for PAPI v1 or cromwell.backend.google.pipelines.v2alpha1.Pipel$nesApiLifecycleActorFactory for PAPI v2
  9. [2018-09-21 20:02:36,65] [ESC[38;5;220mwarnESC[0m] Couldn't find a suitable DSN, defaulting to a Noop one.
  10. [2018-09-21 20:02:36,66] [info] Using noop to send events.
  11. [2018-09-21 20:02:37,03] [info] Slf4jLogger started
  12. [2018-09-21 20:02:37,33] [info] Workflow heartbeat configuration:
  13. {
  14. "cromwellId" : "cromid-6252614",
  15. "heartbeatInterval" : "2 minutes",
  16. "ttl" : "10 minutes",
  17. "writeBatchSize" : 10000,
  18. "writeThreshold" : 10000
  19. }
  20. [2018-09-21 20:02:37,57] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
  21. [2018-09-21 20:02:37,61] [info] Metadata summary refreshing every 2 seconds.
  22. [2018-09-21 20:02:37,77] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
  23. [2018-09-21 20:02:37,81] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
  24. [2018-09-21 20:02:40,83] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
  25. [2018-09-21 20:02:40,93] [info] SingleWorkflowRunnerActor: Version 34
  26. [2018-09-21 20:02:40,96] [info] SingleWorkflowRunnerActor: Submitting workflow
  27. [2018-09-21 20:02:40,98] [info] JES batch polling interval is 33333 milliseconds
  28. [2018-09-21 20:02:40,99] [info] JES batch polling interval is 33333 milliseconds
  29. [2018-09-21 20:02:41,01] [info] JES batch polling interval is 33333 milliseconds
  30. [2018-09-21 20:02:41,05] [info] PAPIQueryManager Running with 3 workers
  31. [2018-09-21 20:02:41,07] [info] Unspecified type (Unspecified version) workflow bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec submitted
  32. [2018-09-21 20:02:41,35] [info] SingleWorkflowRunnerActor: Workflow submitted ESC[38;5;2mbb6365e3-f3d7-4fb6-a5ac-7bb61a55bfecESC[0m
  33. [2018-09-21 20:02:41,37] [ESC[38;5;220mwarnESC[0m] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData
  34. [2018-09-21 20:02:41,41] [info] 1 new workflows fetched
  35. [2018-09-21 20:02:41,41] [info] WorkflowManagerActor Starting workflow ESC[38;5;2mbb6365e3-f3d7-4fb6-a5ac-7bb61a55bfecESC[0m
  36. [2018-09-21 20:02:41,41] [info] WorkflowManagerActor Successfully started WorkflowActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec
  37. [2018-09-21 20:02:41,41] [info] Retrieved 1 workflows from the WorkflowStoreActor
  38. [2018-09-21 20:02:41,43] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
  39. [2018-09-21 20:02:42,12] [info] MaterializeWorkflowDescriptorActor [ESC[38;5;2mbb6365e3ESC[0m]: Parsing workflow as WDL draft-2
  40. [2018-09-21 20:03:04,60] [info] MaterializeWorkflowDescriptorActor [ESC[38;5;2mbb6365e3ESC[0m]: Call-to-Backend assignments: atac.bam2ta -> slurm, atac.idr -> slurm, atac.read_genome_tsv -> slurm, atac.trim_adapter -> slurm, atac.macs2_p
  41. ooled -> slurm, atac.overlap -> slurm, atac.ataqc -> slurm, atac.pool_ta_pr1 -> slurm, atac.macs2 -> slurm, atac.bowtie2 -> slurm, atac.spr -> slurm, atac.qc_report -> slurm, atac.overlap_pr -> slurm, atac.macs2_pr1 -> slurm, atac.pool_t
  42. a -> slurm, atac.macs2_ppr1 -> slurm, atac.macs2_pr2 -> slurm, atac.xcor -> slurm, atac.reproducibility_idr -> slurm, atac.filter -> slurm, atac.idr_pr -> slurm, atac.pool_ta_pr2 -> slurm, atac.macs2_ppr2 -> slurm, atac.idr_ppr -> slurm,
  43. atac.overlap_ppr -> slurm, atac.reproducibility_overlap -> slurm
  44. [2018-09-21 20:03:05,10] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  45. [2018-09-21 20:03:05,16] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  46. [2018-09-21 20:03:05,16] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  47. [2018-09-21 20:03:05,17] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  48. [2018-09-21 20:03:05,21] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  49. [2018-09-21 20:03:05,24] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  50. [2018-09-21 20:03:05,25] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  51. [2018-09-21 20:03:05,26] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  52. [2018-09-21 20:03:05,26] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  53. [2018-09-21 20:03:05,27] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [preemptible, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  54. [2018-09-21 20:03:05,27] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  55. [2018-09-21 20:03:05,27] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  56. [2018-09-21 20:03:05,27] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  57. [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  58. [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  59. [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  60. [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  61. [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  62. [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  63. [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  64. [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  65. [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  66. [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  67. [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  68. [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  69. [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  70. [2018-09-21 20:03:07,66] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Starting atac.read_genome_tsv
  71. [2018-09-21 20:03:07,66] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: '!align_only && !true_rep_only && enable_idr'. Running conditional section
  72. [2018-09-21 20:03:07,67] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: '!true_rep_only'. Running conditional section
  73. [2018-09-21 20:03:07,70] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: 'enable_idr'. Running conditional section
  74. [2018-09-21 20:03:07,70] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: '!disable_xcor'. Running conditional section
  75. [2018-09-21 20:03:07,70] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: '!align_only && !true_rep_only'. Running conditional section
  76. [2018-09-21 20:03:07,71] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: 'enable_idr'. Running conditional section
  77. [2018-09-21 20:03:08,06] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: Unrecognized runtime attribute keys: disks
  78. [2018-09-21 20:03:09,55] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: ESC[38;5;5mcat /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv/inputs/378634365/hg19.tsvESC[0m
  79. [2018-09-21 20:03:09,61] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: executing: sbatch \
  80. --export=ALL \
  81. -J cromwell_bb6365e3_read_genome_tsv \
  82. -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv \
  83. -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv/execution/stdout \
  84. -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv/execution/stderr \
  85. -t 60 \
  86. -n 1 \
  87. --ntasks-per-node=1 \
  88. --cpus-per-task=1 \
  89. --mem=4000 \
  90. -p broadwl \
  91. \
  92. --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv/execution/script"
  93. [2018-09-21 20:03:12,42] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Starting atac.trim_adapter (2 shards)
  94. [2018-09-21 20:03:12,63] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: job id: 49925419
  95. [2018-09-21 20:03:12,65] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: Status change from - to WaitingForReturnCodeFile
  96. [2018-09-21 20:03:12,90] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: Unrecognized runtime attribute keys: disks
  97. [2018-09-21 20:03:12,92] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: Unrecognized runtime attribute keys: disks
  98. [2018-09-21 20:03:13,33] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: ESC[38;5;5mpython $(which encode_trim_adapter.py) \
  99. /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/write_tsv_3274ebda6c46dc57a250f066328e4929.tmp \
  100. --adapters /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/write_tsv_d41d8cd98f00b204e9800998ecf8427e.tmp \
  101. --paired-end \
  102. --auto-detect-adapter \
  103. --min-trim-len 5 \
  104. --err-rate 0.1 \
  105. --nth 1ESC[0m
  106. [2018-09-21 20:03:13,36] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: ESC[38;5;5mpython $(which encode_trim_adapter.py) \
  107. /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/write_tsv_4ec997f74112c76af08be107c84bd1f0.tmp \
  108. --adapters /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/write_tsv_d41d8cd98f00b204e9800998ecf8427e.tmp \
  109. --paired-end \
  110. --auto-detect-adapter \
  111. --min-trim-len 5 \
  112. --err-rate 0.1 \
  113. --nth 1ESC[0m
  114. [2018-09-21 20:03:13,41] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: executing: sbatch \
  115. --export=ALL \
  116. -J cromwell_bb6365e3_trim_adapter \
  117. -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0 \
  118. -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/stdout \
  119. -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/stderr \
  120. -t 1440 \
  121. -n 1 \
  122. --ntasks-per-node=1 \
  123. --cpus-per-task=1 \
  124. --mem=12000 \
  125. -p broadwl \
  126. \
  127. --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/script"
  128. [2018-09-21 20:03:13,47] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: executing: sbatch \
  129. --export=ALL \
  130. -J cromwell_bb6365e3_trim_adapter \
  131. -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1 \
  132. -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/stdout \
  133. -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/stderr \
  134. -t 1440 \
  135. -n 1 \
  136. --ntasks-per-node=1 \
  137. --cpus-per-task=1 \
  138. --mem=12000 \
  139. -p broadwl \
  140. \
  141. --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/script"
  142. [2018-09-21 20:03:17,62] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: job id: 49925421
  143. [2018-09-21 20:03:17,64] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: job id: 49925422
  144. [2018-09-21 20:03:17,64] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: Status change from - to WaitingForReturnCodeFile
  145. [2018-09-21 20:03:17,66] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: Status change from - to WaitingForReturnCodeFile
  146. [2018-09-21 20:04:24,26] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: Status change from WaitingForReturnCodeFile to Done
  147. [2018-09-21 20:05:48,94] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: Status change from WaitingForReturnCodeFile to Done
  148. [2018-09-21 20:05:50,22] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Starting atac.bowtie2
  149. [2018-09-21 20:05:50,85] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:0:1]: Unrecognized runtime attribute keys: preemptible, disks
  150. [2018-09-21 20:05:50,87] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: Status change from WaitingForReturnCodeFile to Done
  151. [2018-09-21 20:05:50,91] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:0:1]: ESC[38;5;5mpython $(which encode_bowtie2.py) \
  152. /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/inputs/646531885/male.hg19.fa.tar \
  153. /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/inputs/-1650399814/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.fastq.gz /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/inputs/-1650399814/merge_fastqs_R2_ENCFF248EJF.subsampled.400.trim.merged.fastq.gz \
  154. --paired-end \
  155. --multimapping 4 \
  156. \
  157. --nth 2ESC[0m
  158. [2018-09-21 20:05:51,79] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:0:1]: executing: sbatch \
  159. --export=ALL \
  160. -J cromwell_bb6365e3_bowtie2 \
  161. -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0 \
  162. -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/execution/stdout \
  163. -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/execution/stderr \
  164. -t 2880 \
  165. -n 1 \
  166. --ntasks-per-node=1 \
  167. --cpus-per-task=2 \
  168. --mem=16000 \
  169. -p broadwl \
  170. \
  171. --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/execution/script"
  172. [2018-09-21 20:05:52,27] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Starting atac.bowtie2
  173. [2018-09-21 20:05:52,90] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:1:1]: Unrecognized runtime attribute keys: preemptible, disks
  174. [2018-09-21 20:05:53,00] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:1:1]: ESC[38;5;5mpython $(which encode_bowtie2.py) \
  175. /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/inputs/646531885/male.hg19.fa.tar \
  176. /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/inputs/-1658159173/merge_fastqs_R1_ENCFF641SFZ.subsampled.400.trim.merged.fastq.gz /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/inputs/-1658159173/merge_fastqs_R2_ENCFF031ARQ.subsampled.400.trim.merged.fastq.gz \
  177. --paired-end \
  178. --multimapping 4 \
  179. \
  180. --nth 2ESC[0m
  181. [2018-09-21 20:05:53,08] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:1:1]: executing: sbatch \
  182. --export=ALL \
  183. -J cromwell_bb6365e3_bowtie2 \
  184. -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1 \
  185. -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/execution/stdout \
  186. -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/execution/stderr \
  187. -t 2880 \
  188. -n 1 \
  189. --ntasks-per-node=1 \
  190. --cpus-per-task=2 \
  191. --mem=16000 \
  192. -p broadwl \
  193. \
  194. --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/execution/script"
  195. [2018-09-21 20:05:55,36] [ESC[38;5;1merrorESC[0m] WorkflowManagerActor Workflow bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec failed (during ExecutingWorkflowState): java.lang.RuntimeException: Unable to start job. Check the stderr file for possi
  196. ble errors: /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/execution/stderr.submit
  197. at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.$anonfun$execute$2(SharedFileSystemAsyncJobExecutionActor.scala:131)
  198. at scala.util.Either.fold(Either.scala:188)
  199. at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:126)
  200. at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
  201. at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:208)
  202. at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
  203. at scala.util.Try$.apply(Try.scala:209)
  204. at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
  205. at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
  206. at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:208)
  207. at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
  208. at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
  209. at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:208)
  210. at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
  211. at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
  212. at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:61)
  213. at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:65)
  214. at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:88)
  215. at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
  216. at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
  217. at akka.actor.Actor.aroundReceive(Actor.scala:517)
  218. at akka.actor.Actor.aroundReceive$(Actor.scala:515)
  219. at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:208)
  220. at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
  221. at akka.actor.ActorCell.invoke(ActorCell.scala:557)
  222. at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
  223. at akka.dispatch.Mailbox.run(Mailbox.scala:225)
  224. at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
  225. at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
  226. at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
  227. at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
  228. at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
  229.  
  230. java.lang.RuntimeException: Unable to start job. Check the stderr file for possible errors: /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/execution/stderr.submit
  231. at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.$anonfun$execute$2(SharedFileSystemAsyncJobExecutionActor.scala:131)
  232. at scala.util.Either.fold(Either.scala:188)
  233. at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:126)
  234. at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
  235. at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:208)
  236. at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
  237. at scala.util.Try$.apply(Try.scala:209)
  238. at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
  239. at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
  240. at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:208)
  241. at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
  242. at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
  243. at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:208)
  244. at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
  245. at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
  246. at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:61)
  247. at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:65)
  248. at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:88)
  249. at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
  250. at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
  251. at akka.actor.Actor.aroundReceive(Actor.scala:517)
  252. at akka.actor.Actor.aroundReceive$(Actor.scala:515)
  253. at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:208)
  254. at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
  255. at akka.actor.ActorCell.invoke(ActorCell.scala:557)
  256. at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
  257. at akka.dispatch.Mailbox.run(Mailbox.scala:225)
  258. at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
  259. at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
  260. at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
  261. at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
  262. at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
  263.  
  264. [2018-09-21 20:05:55,37] [info] WorkflowManagerActor WorkflowActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec is in a terminal state: WorkflowFailedState
  265. [2018-09-21 20:06:04,87] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
  266. [2018-09-21 20:06:07,83] [info] Workflow polling stopped
  267. [2018-09-21 20:06:07,84] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
  268. [2018-09-21 20:06:07,85] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
  269. [2018-09-21 20:06:07,87] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
  270. [2018-09-21 20:06:07,88] [info] JobExecutionTokenDispenser stopped
  271. [2018-09-21 20:06:07,89] [info] WorkflowStoreActor stopped
  272. [2018-09-21 20:06:07,88] [info] Aborting all running workflows.
  273. [2018-09-21 20:06:07,90] [info] WorkflowLogCopyRouter stopped
  274. [2018-09-21 20:06:07,90] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
  275. [2018-09-21 20:06:07,90] [info] WorkflowManagerActor All workflows finished
  276. [2018-09-21 20:06:07,91] [info] WorkflowManagerActor stopped
  277. [2018-09-21 20:06:07,91] [info] Connection pools shut down
  278. [2018-09-21 20:06:07,91] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
  279. [2018-09-21 20:06:07,91] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
  280. [2018-09-21 20:06:07,91] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
  281. [2018-09-21 20:06:07,91] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
  282. [2018-09-21 20:06:07,91] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
  283. [2018-09-21 20:06:07,91] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
  284. [2018-09-21 20:06:07,91] [info] Shutting down IoProxy - Timeout = 1800 seconds
  285. [2018-09-21 20:06:07,91] [info] SubWorkflowStoreActor stopped
  286. [2018-09-21 20:06:07,91] [info] JobStoreActor stopped
  287. [2018-09-21 20:06:07,91] [info] CallCacheWriteActor stopped
  288. [2018-09-21 20:06:07,91] [info] DockerHashActor stopped
  289. [2018-09-21 20:06:07,91] [info] IoProxy stopped
  290. [2018-09-21 20:06:07,92] [info] WriteMetadataActor Shutting down: 0 queued messages to process
  291. [2018-09-21 20:06:07,92] [info] KvWriteActor Shutting down: 0 queued messages to process
  292. [2018-09-21 20:06:07,92] [info] ServiceRegistryActor stopped
  293. [2018-09-21 20:06:07,96] [info] Database closed
  294. [2018-09-21 20:06:07,96] [info] Stream materializer shut down
  295. Workflow bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec transitioned to state Failed
  296. [2018-09-21 20:06:08,05] [info] Automatic shutdown of the async connection
  297. [2018-09-21 20:06:08,05] [info] Gracefully shutdown sentry threads.
  298. [2018-09-21 20:06:08,07] [info] Shutdown finished.
  299. ```
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