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  1. 2019-01-16 11:36:18,622 INFO - MaterializeWorkflowDescriptorActor [UUID(0627e8c3)]: Parsing workflow as WDL draft-2
  2. 2019-01-16 11:37:27,526 INFO - MaterializeWorkflowDescriptorActor [UUID(0627e8c3)]: Call-to-Backend assignments: chip.overlap -> Local, chip.macs2_ppr2 -> Local, chip.merge_fastq_ctl -> Local, chip.overlap_pr -> Local, chip.pool_ta_pr2 -> Local, chip.spp_ppr2 -> Local, chip.bam2ta -> Local, chip.xcor -> Local, chip.reproducibility_idr -> Local, chip.overlap_ppr -> Local, chip.bwa_ctl -> Local, chip.idr -> Local, chip.macs2_pr2 -> Local, chip.bam2ta_no_filt -> Local, chip.bwa_R1 -> Local, chip.reproducibility_overlap -> Local, chip.spp_pr1 -> Local, chip.bam2ta_ctl -> Local, chip.trim_fastq -> Local, chip.fraglen_mean -> Local, chip.idr_pr -> Local, chip.fingerprint -> Local, chip.read_genome_tsv -> Local, chip.spp_pooled -> Local, chip.filter -> Local, chip.macs2_pr1 -> Local, chip.bwa -> Local, chip.spp_ppr1 -> Local, chip.bam2ta_no_filt_R1 -> Local, chip.merge_fastq -> Local, chip.pool_ta_ctl -> Local, chip.macs2_ppr1 -> Local, chip.spp_pr2 -> Local, chip.idr_ppr -> Local, chip.qc_report -> Local, chip.pool_ta -> Local, chip.spp -> Local, chip.filter_ctl -> Local, chip.choose_ctl -> Local, chip.pool_ta_pr1 -> Local, chip.spr -> Local, chip.macs2_pooled -> Local, chip.macs2 -> Local
  3. 2019-01-16 11:37:27,744 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  4. 2019-01-16 11:37:27,748 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  5. 2019-01-16 11:37:27,751 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  6. 2019-01-16 11:37:27,752 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  7. 2019-01-16 11:37:27,754 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  8. 2019-01-16 11:37:27,756 WARN - Local [UUID(0627e8c3)]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  9. 2019-01-16 11:37:27,761 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  10. 2019-01-16 11:37:27,763 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  11. 2019-01-16 11:37:27,764 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  12. 2019-01-16 11:37:27,769 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  13. 2019-01-16 11:37:27,769 WARN - Local [UUID(0627e8c3)]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  14. 2019-01-16 11:37:27,774 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  15. 2019-01-16 11:37:27,774 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  16. 2019-01-16 11:37:27,780 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  17. 2019-01-16 11:37:27,780 WARN - Local [UUID(0627e8c3)]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  18. 2019-01-16 11:37:27,781 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  19. 2019-01-16 11:37:27,781 WARN - Local [UUID(0627e8c3)]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  20. 2019-01-16 11:37:27,781 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  21. 2019-01-16 11:37:27,782 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  22. 2019-01-16 11:37:27,782 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  23. 2019-01-16 11:37:27,782 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  24. 2019-01-16 11:37:27,782 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  25. 2019-01-16 11:37:27,783 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  26. 2019-01-16 11:37:27,783 WARN - Local [UUID(0627e8c3)]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  27. 2019-01-16 11:37:27,783 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  28. 2019-01-16 11:37:27,783 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  29. 2019-01-16 11:37:27,784 WARN - Local [UUID(0627e8c3)]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  30. 2019-01-16 11:37:27,784 WARN - Local [UUID(0627e8c3)]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  31. 2019-01-16 11:37:27,784 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  32. 2019-01-16 11:37:27,784 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  33. 2019-01-16 11:37:27,810 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  34. 2019-01-16 11:37:27,810 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  35. 2019-01-16 11:37:27,811 WARN - Local [UUID(0627e8c3)]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  36. 2019-01-16 11:37:27,811 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  37. 2019-01-16 11:37:27,821 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  38. 2019-01-16 11:37:27,821 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  39. 2019-01-16 11:37:27,822 WARN - Local [UUID(0627e8c3)]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  40. 2019-01-16 11:37:27,822 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  41. 2019-01-16 11:37:27,822 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  42. 2019-01-16 11:37:27,822 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  43. 2019-01-16 11:37:27,823 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  44. 2019-01-16 11:37:27,823 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  45. 2019-01-16 11:37:27,823 WARN - Local [UUID(0627e8c3)]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
  46. 2019-01-16 11:37:30,722 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Starting chip.read_genome_tsv
  47. 2019-01-16 11:37:30,725 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: '!align_only && !true_rep_only'. Running conditional section
  48. 2019-01-16 11:37:30,749 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: '!true_rep_only'. Running conditional section
  49. 2019-01-16 11:37:31,861 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: '!align_only && !true_rep_only && enable_idr'. Running conditional section
  50. 2019-01-16 11:37:31,863 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition NOT met: 'peak_caller_ == "macs2"'. Bypassing conditional section
  51. 2019-01-16 11:37:31,889 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: 'enable_idr'. Running conditional section
  52. 2019-01-16 11:37:31,891 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: 'enable_idr'. Running conditional section
  53. 2019-01-16 11:37:31,933 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: 'peak_caller_ == "spp"'. Running conditional section
  54. 2019-01-16 11:37:31,935 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: 'peak_caller_ == "spp"'. Running conditional section
  55. 2019-01-16 11:37:32,097 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.read_genome_tsv:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  56. 2019-01-16 11:37:32,930 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.read_genome_tsv:NA:1]: `cat /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-read_genome_tsv/inputs/-1845944697/hg38_local.tsv > 'tmp.tsv'`
  57. 2019-01-16 11:37:33,092 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.read_genome_tsv:NA:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-read_genome_tsv/execution/script
  58. 2019-01-16 11:37:35,158 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.read_genome_tsv:NA:1]: job id: 24017
  59. 2019-01-16 11:37:35,167 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.read_genome_tsv:NA:1]: Status change from - to Done
  60. 2019-01-16 11:37:41,274 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: '!disable_fingerprint && length(nodup_bams_) > 0 && length(ctl_nodup_bams_) > 0 && basename(blacklist) != "null"'. Running conditional section
  61. 2019-01-16 11:37:43,343 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Starting chip.bam2ta_ctl, chip.bam2ta, chip.fingerprint
  62. 2019-01-16 11:37:43,662 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta_ctl:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  63. 2019-01-16 11:37:43,679 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  64. 2019-01-16 11:37:43,692 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fingerprint:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  65. 2019-01-16 11:37:43,747 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta:0:1]: `python $(which encode_bam2ta.py) \
  66. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-bam2ta/shard-0/inputs/1101703518/1218HS_10_S23rmDu_sorted.bam \
  67. --disable-tn5-shift \
  68. --paired-end \
  69. --regex-grep-v-ta 'chrM' \
  70. --subsample 0 \
  71. --nth 2`
  72. 2019-01-16 11:37:43,754 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta_ctl:0:1]: `python $(which encode_bam2ta.py) \
  73. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-bam2ta_ctl/shard-0/inputs/1101703518/1218HS_1_S14rmDu_sorted.bam \
  74. --disable-tn5-shift \
  75. --paired-end \
  76. --regex-grep-v-ta 'chrM' \
  77. --subsample 0 \
  78. --nth 2`
  79. 2019-01-16 11:37:43,790 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fingerprint:NA:1]: `python $(which encode_fingerprint.py) \
  80. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-fingerprint/inputs/1101703518/1218HS_10_S23rmDu_sorted.bam \
  81. --ctl-bam /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-fingerprint/inputs/1101703518/1218HS_1_S14rmDu_sorted.bam \
  82. --blacklist /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-fingerprint/inputs/-600900052/hg38.blacklist.bed.gz \
  83. --nth 2`
  84. 2019-01-16 11:37:43,804 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta_ctl:0:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-bam2ta_ctl/shard-0/execution/script
  85. 2019-01-16 11:37:43,807 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta:0:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-bam2ta/shard-0/execution/script
  86. 2019-01-16 11:37:43,830 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fingerprint:NA:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-fingerprint/execution/script
  87. 2019-01-16 11:37:45,219 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fingerprint:NA:1]: job id: 24082
  88. 2019-01-16 11:37:45,219 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta_ctl:0:1]: job id: 24080
  89. 2019-01-16 11:37:45,230 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta:0:1]: job id: 24081
  90. 2019-01-16 11:37:45,239 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta_ctl:0:1]: Status change from - to WaitingForReturnCodeFile
  91. 2019-01-16 11:37:45,241 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta:0:1]: Status change from - to WaitingForReturnCodeFile
  92. 2019-01-16 11:37:45,243 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fingerprint:NA:1]: Status change from - to WaitingForReturnCodeFile
  93. 2019-01-16 14:13:49,874 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta:0:1]: Status change from WaitingForReturnCodeFile to Done
  94. 2019-01-16 14:13:53,451 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition NOT met: '!true_rep_only && length(tas_) > 1'. Bypassing conditional section
  95. 2019-01-16 14:13:53,455 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition NOT met: '!true_rep_only && length(tas_) > 1 && peak_caller_ == "spp"'. Bypassing conditional section
  96. 2019-01-16 14:13:53,457 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition NOT met: 'length(tas_) > 1 && peak_caller_ == "spp"'. Bypassing conditional section
  97. 2019-01-16 14:13:53,459 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition NOT met: '!true_rep_only && length(tas_) > 1 && peak_caller_ == "macs2"'. Bypassing conditional section
  98. 2019-01-16 14:13:53,464 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition NOT met: 'length(tas_) > 1'. Bypassing conditional section
  99. 2019-01-16 14:13:53,473 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition NOT met: '!true_rep_only && length(tas_) > 1 && peak_caller_ == "macs2"'. Bypassing conditional section
  100. 2019-01-16 14:13:53,488 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition NOT met: 'length(tas_) > 1'. Bypassing conditional section
  101. 2019-01-16 14:13:53,503 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition NOT met: '!true_rep_only && length(tas_) > 1 && peak_caller_ == "spp"'. Bypassing conditional section
  102. 2019-01-16 14:13:55,874 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Starting chip.xcor, chip.spr
  103. 2019-01-16 14:13:56,656 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spr:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  104. 2019-01-16 14:13:56,672 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.xcor:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  105. 2019-01-16 14:13:56,726 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spr:0:1]: `python $(which encode_spr.py) \
  106. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spr/shard-0/inputs/1646945325/1218HS_10_S23rmDu_sorted.tagAlign.gz \
  107. --paired-end`
  108. 2019-01-16 14:13:56,732 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.xcor:0:1]: `python $(which encode_xcor.py) \
  109. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-xcor/shard-0/inputs/1646945325/1218HS_10_S23rmDu_sorted.tagAlign.gz \
  110. --paired-end \
  111. --subsample 15000000 \
  112. --nth 2`
  113. 2019-01-16 14:13:56,810 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spr:0:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spr/shard-0/execution/script
  114. 2019-01-16 14:13:56,853 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.xcor:0:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-xcor/shard-0/execution/script
  115. 2019-01-16 14:14:00,055 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.xcor:0:1]: job id: 47819
  116. 2019-01-16 14:14:00,055 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spr:0:1]: job id: 47818
  117. 2019-01-16 14:14:00,060 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.xcor:0:1]: Status change from - to WaitingForReturnCodeFile
  118. 2019-01-16 14:14:00,060 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spr:0:1]: Status change from - to WaitingForReturnCodeFile
  119. 2019-01-16 14:15:47,171 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.bam2ta_ctl:0:1]: Status change from WaitingForReturnCodeFile to Done
  120. 2019-01-16 14:15:51,143 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: 'length(tas_) > 0 && length(ctl_tas_) > 0'. Running conditional section
  121. 2019-01-16 14:15:51,143 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Condition met: 'length(ctl_tas_) > 0'. Running conditional section
  122. 2019-01-16 14:15:53,192 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Starting chip.pool_ta_ctl
  123. 2019-01-16 14:15:53,647 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.pool_ta_ctl:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  124. 2019-01-16 14:15:53,661 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.pool_ta_ctl:NA:1]: `python $(which encode_pool_ta.py) \
  125. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-pool_ta_ctl/inputs/-338498295/1218HS_1_S14rmDu_sorted.tagAlign.gz`
  126. 2019-01-16 14:15:53,690 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.pool_ta_ctl:NA:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-pool_ta_ctl/execution/script
  127. 2019-01-16 14:15:55,047 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.pool_ta_ctl:NA:1]: job id: 48150
  128. 2019-01-16 14:15:55,052 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.pool_ta_ctl:NA:1]: Status change from - to WaitingForReturnCodeFile
  129. 2019-01-16 14:15:57,231 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.pool_ta_ctl:NA:1]: Status change from WaitingForReturnCodeFile to Done
  130. 2019-01-16 14:16:00,332 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Starting chip.choose_ctl
  131. 2019-01-16 14:16:00,648 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.choose_ctl:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  132. 2019-01-16 14:16:00,713 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.choose_ctl:NA:1]: `python $(which encode_choose_ctl.py) \
  133. --tas /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-choose_ctl/inputs/1646945325/1218HS_10_S23rmDu_sorted.tagAlign.gz \
  134. --ctl-tas /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-choose_ctl/inputs/-338498295/1218HS_1_S14rmDu_sorted.tagAlign.gz \
  135. \
  136. --ctl-ta-pooled /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-choose_ctl/inputs/-895249818/1218HS_1_S14rmDu_sorted.tagAlign.gz \
  137. --always-use-pooled-ctl \
  138. --ctl-depth-ratio 1.2`
  139. 2019-01-16 14:16:00,737 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.choose_ctl:NA:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-choose_ctl/execution/script
  140. 2019-01-16 14:16:05,046 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.choose_ctl:NA:1]: job id: 48193
  141. 2019-01-16 14:16:05,057 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.choose_ctl:NA:1]: Status change from - to WaitingForReturnCodeFile
  142. 2019-01-16 14:16:15,182 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.choose_ctl:NA:1]: Status change from WaitingForReturnCodeFile to Done
  143. 2019-01-16 14:22:26,760 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fingerprint:NA:1]: Status change from WaitingForReturnCodeFile to Done
  144. 2019-01-16 14:29:35,283 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spr:0:1]: Status change from WaitingForReturnCodeFile to Done
  145. 2019-01-16 15:18:37,773 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.xcor:0:1]: Status change from WaitingForReturnCodeFile to Done
  146. 2019-01-16 15:18:41,782 INFO - WorkflowExecutionActor-0627e8c3-15f3-4dd7-99ff-dd6f07cd5874 [UUID(0627e8c3)]: Starting chip.spp_pr1, chip.fraglen_mean, chip.spp_pr2, chip.spp, chip.macs2
  147. 2019-01-16 15:18:42,657 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.macs2:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  148. 2019-01-16 15:18:42,659 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr1:0:1]: Unrecognized runtime attribute keys: preemptible, disks, cpu, time, memory
  149. 2019-01-16 15:18:42,660 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fraglen_mean:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
  150. 2019-01-16 15:18:42,668 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp:0:1]: Unrecognized runtime attribute keys: preemptible, disks, cpu, time, memory
  151. 2019-01-16 15:18:42,674 WARN - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr2:0:1]: Unrecognized runtime attribute keys: preemptible, disks, cpu, time, memory
  152. 2019-01-16 15:18:42,682 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fraglen_mean:NA:1]: `python <<CODE
  153. arr = [220]
  154. with open('tmp.txt','w') as fp:
  155. if len(arr):
  156. sum_ = sum(arr)
  157. mean_ = sum(arr)/float(len(arr))
  158. fp.write('{}'.format(int(round(mean_))))
  159. else:
  160. fp.write('0')
  161. CODE`
  162. 2019-01-16 15:18:42,723 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr2:0:1]: `python $(which encode_spp.py) \
  163. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr2/shard-0/inputs/-1510458860/1218HS_10_S23rmDu_sorted.pr2.tagAlign.gz /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr2/shard-0/inputs/415375928/ctl_for_rep1.tagAlign.gz \
  164. --chrsz /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr2/shard-0/inputs/-600900052/hg38.chrom.sizes \
  165. --fraglen 220 \
  166. --cap-num-peak 300000 \
  167. --nth 2 \
  168. \
  169. --blacklist /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr2/shard-0/inputs/-600900052/hg38.blacklist.bed.gz`
  170. 2019-01-16 15:18:42,729 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp:0:1]: `python $(which encode_spp.py) \
  171. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp/shard-0/inputs/1646945325/1218HS_10_S23rmDu_sorted.tagAlign.gz /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp/shard-0/inputs/415375928/ctl_for_rep1.tagAlign.gz \
  172. --chrsz /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp/shard-0/inputs/-600900052/hg38.chrom.sizes \
  173. --fraglen 220 \
  174. --cap-num-peak 300000 \
  175. --nth 2 \
  176. \
  177. --blacklist /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp/shard-0/inputs/-600900052/hg38.blacklist.bed.gz`
  178. 2019-01-16 15:18:42,749 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr1:0:1]: `python $(which encode_spp.py) \
  179. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr1/shard-0/inputs/453162443/1218HS_10_S23rmDu_sorted.pr1.tagAlign.gz /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr1/shard-0/inputs/415375928/ctl_for_rep1.tagAlign.gz \
  180. --chrsz /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr1/shard-0/inputs/-600900052/hg38.chrom.sizes \
  181. --fraglen 220 \
  182. --cap-num-peak 300000 \
  183. --nth 2 \
  184. \
  185. --blacklist /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr1/shard-0/inputs/-600900052/hg38.blacklist.bed.gz`
  186. 2019-01-16 15:18:42,769 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.macs2:0:1]: `
  187. touch null
  188. python $(which encode_macs2_chip.py) \
  189. /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-macs2/shard-0/inputs/1646945325/1218HS_10_S23rmDu_sorted.tagAlign.gz /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-macs2/shard-0/inputs/415375928/ctl_for_rep1.tagAlign.gz \
  190. --gensz hs \
  191. --chrsz /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-macs2/shard-0/inputs/-600900052/hg38.chrom.sizes \
  192. --fraglen 220 \
  193. --cap-num-peak 500000 \
  194. --pval-thresh 0.01 \
  195. --make-signal \
  196. \
  197. --blacklist /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-macs2/shard-0/inputs/-600900052/hg38.blacklist.bed.gz`
  198. 2019-01-16 15:18:42,788 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fraglen_mean:NA:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-fraglen_mean/execution/script
  199. 2019-01-16 15:18:42,837 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr2:0:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr2/shard-0/execution/script
  200. 2019-01-16 15:18:42,841 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp:0:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp/shard-0/execution/script
  201. 2019-01-16 15:18:42,844 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr1:0:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-spp_pr1/shard-0/execution/script
  202. 2019-01-16 15:18:42,917 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.macs2:0:1]: executing: /bin/bash /project/umw_leslie_shaw/Aimin/chip-seq-pipeline2/cromwell-executions/chip/0627e8c3-15f3-4dd7-99ff-dd6f07cd5874/call-macs2/shard-0/execution/script
  203. 2019-01-16 15:18:45,035 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fraglen_mean:NA:1]: job id: 7257
  204. 2019-01-16 15:18:45,035 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr1:0:1]: job id: 7262
  205. 2019-01-16 15:18:45,035 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr2:0:1]: job id: 7261
  206. 2019-01-16 15:18:45,036 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp:0:1]: job id: 7260
  207. 2019-01-16 15:18:45,036 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.macs2:0:1]: job id: 7275
  208. 2019-01-16 15:18:45,115 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr2:0:1]: Status change from - to WaitingForReturnCodeFile
  209. 2019-01-16 15:18:45,116 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp:0:1]: Status change from - to WaitingForReturnCodeFile
  210. 2019-01-16 15:18:45,118 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.macs2:0:1]: Status change from - to WaitingForReturnCodeFile
  211. 2019-01-16 15:18:45,119 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.spp_pr1:0:1]: Status change from - to WaitingForReturnCodeFile
  212. 2019-01-16 15:18:45,120 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.fraglen_mean:NA:1]: Status change from - to Done
  213. 2019-01-16 15:18:48,090 INFO - BackgroundConfigAsyncJobExecutionActor [UUID(0627e8c3)chip.macs2:0:1]: Status change from WaitingForReturnCodeFile to Done
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