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Published 20 hours ago • verified publisher icon broadinstitute

**DO NOT MERGE** assembly changes to test carrot

Open jamesemery opened this issue 2 years ago • 32 comments

jamesemery avatar Mar 15 '22 02:03 jamesemery

Started a CARROT test run : HaplotypeCaller CARROT Regression Tests_run_2022-03-15 02:48:40.559977508 UTC 
 
 {
  "run_id": "3b13e474-9e2d-41cd-b846-c5ed41305f3a",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-15 02:48:40.559977508 UTC",
  "status": "building",
  "test_input": {
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    "VariantCallingCarrotOrchestrated.CHM_base_file_name": "CHM113",
    "VariantCallingCarrotOrchestrated.CHM_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.CHM_contamination": 0.0,
    "VariantCallingCarrotOrchestrated.CHM_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm1_chm13_hiseqx_sm_hf3mo.bam",
    "VariantCallingCarrotOrchestrated.CHM_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.NIST_base_file_name": "NA24385",
    "VariantCallingCarrotOrchestrated.NIST_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.NIST_contamination": 0.0383312,
    "VariantCallingCarrotOrchestrated.NIST_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrotOrchestrated.NIST_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.agg_preemptible_tries": 3,
    "VariantCallingCarrotOrchestrated.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrotOrchestrated.contamination": 0.0,
    "VariantCallingCarrotOrchestrated.exome1_base_file_name": "NA12878Exome1",
    "VariantCallingCarrotOrchestrated.exome1_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_calling_regions.v1.interval_list",
    "VariantCallingCarrotOrchestrated.exome1_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram",
    "VariantCallingCarrotOrchestrated.exome1_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram.crai",
    "VariantCallingCarrotOrchestrated.gatk_control_docker": "broadinstitute/gatk-nightly:2022-03-04-4.2.5.0-9-gb097f75c5-NIGHTLY-SNAPSHOT",
    "VariantCallingCarrotOrchestrated.haplotype_scatter_count": 50,
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    "VariantCallingCarrotOrchestrated.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrotOrchestrated.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrotOrchestrated.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrotOrchestrated.use_gatk3_haplotype_caller": true
  },
  "test_options": null,
  "eval_input": {
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.CHM_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.CHM_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.CHM_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.CHM_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthLabel": "CHM_GRCh38_SYNDIPv20180222",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.twist_exome.interval_list",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthLabel": "NA12878_GRCh38_TWISTExome",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
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    "BenchmarkVCFsHeadToHeadOrchestrated.hapMap": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkVCFsHeadToHeadOrchestrated.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkVCFsHeadToHeadOrchestrated.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
    "BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HCR_hg38.bed",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCR_Hg38.interval_list"
    ],
    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
      "HCR",
      "LCR"
    ]
  },
  "eval_options": null,
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-03-15T02:48:40.560051",
  "created_by": null,
  "finished_at": null
}

CarrotBroadBot avatar Mar 15 '22 02:03 CarrotBroadBot

CARROT test run finished 
 
 {
  "run_id": "3b13e474-9e2d-41cd-b846-c5ed41305f3a",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-15 02:48:40.559977508 UTC",
  "status": "testfailed",
  "test_input": {
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    "VariantCallingCarrotOrchestrated.CHM_base_file_name": "CHM113",
    "VariantCallingCarrotOrchestrated.CHM_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.CHM_contamination": 0.0,
    "VariantCallingCarrotOrchestrated.CHM_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm1_chm13_hiseqx_sm_hf3mo.bam",
    "VariantCallingCarrotOrchestrated.CHM_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.NIST_base_file_name": "NA24385",
    "VariantCallingCarrotOrchestrated.NIST_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
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    "VariantCallingCarrotOrchestrated.NIST_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
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    "VariantCallingCarrotOrchestrated.contamination": 0.0,
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    "VariantCallingCarrotOrchestrated.use_gatk3_haplotype_caller": true
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  "test_options": null,
  "eval_input": {
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    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalLabel": "TESTSNAPSHOT2018HG002",
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    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthLabel": "NA12878_GRCh38_TWISTExome",
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    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.hapMap": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkVCFsHeadToHeadOrchestrated.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkVCFsHeadToHeadOrchestrated.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
    "BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HCR_hg38.bed",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCR_Hg38.interval_list"
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    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
      "HCR",
      "LCR"
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  },
  "eval_options": null,
  "test_cromwell_job_id": "d0d7d45a-32df-48b1-b296-54d81f32bc02",
  "eval_cromwell_job_id": null,
  "created_at": "2022-03-15T02:48:40.560051",
  "created_by": null,
  "finished_at": "2022-03-15T17:06:51.310",
  "results": null
}

CarrotBroadBot avatar Mar 15 '22 17:03 CarrotBroadBot

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Mar 15 '22 18:03 jamesemery

Started a CARROT test run : HaplotypeCaller CARROT Regression Tests_run_2022-03-15 18:03:51.605578569 UTC 
 
 {
  "run_id": "ea93cfbf-57fe-4ca6-bf87-78535e66ffb2",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-15 18:03:51.605578569 UTC",
  "status": "building",
  "test_input": {
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    "VariantCallingCarrotOrchestrated.CHM_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.CHM_contamination": 0.0,
    "VariantCallingCarrotOrchestrated.CHM_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm1_chm13_hiseqx_sm_hf3mo.bam",
    "VariantCallingCarrotOrchestrated.CHM_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.NIST_base_file_name": "NA24385",
    "VariantCallingCarrotOrchestrated.NIST_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.NIST_contamination": 0.0383312,
    "VariantCallingCarrotOrchestrated.NIST_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrotOrchestrated.NIST_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.agg_preemptible_tries": 3,
    "VariantCallingCarrotOrchestrated.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrotOrchestrated.contamination": 0.0,
    "VariantCallingCarrotOrchestrated.exome1_base_file_name": "NA12878Exome1",
    "VariantCallingCarrotOrchestrated.exome1_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_calling_regions.v1.interval_list",
    "VariantCallingCarrotOrchestrated.exome1_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram",
    "VariantCallingCarrotOrchestrated.exome1_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram.crai",
    "VariantCallingCarrotOrchestrated.gatk_control_docker": "broadinstitute/gatk-nightly:2022-03-04-4.2.5.0-9-gb097f75c5-NIGHTLY-SNAPSHOT",
    "VariantCallingCarrotOrchestrated.gatk_docker": "image_build:gatk|0a267ad11c3612a61464a84a0ead0d4d89a0ff0b",
    "VariantCallingCarrotOrchestrated.haplotype_scatter_count": 50,
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    "VariantCallingCarrotOrchestrated.use_gatk3_haplotype_caller": true
  },
  "test_options": null,
  "eval_input": {
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlLabel": "CONTROLSNAPSHOT2018HG002",
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.CHM_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalLabel": "TESTSNAPSHOT2018HG002",
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.CHM_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthLabel": "CHM_GRCh38_SYNDIPv20180222",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.twist_exome.interval_list",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlLabel": "CONTROLSNAPSHOT2018HG002",
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    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthLabel": "NA12878_GRCh38_TWISTExome",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.hapMap": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkVCFsHeadToHeadOrchestrated.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkVCFsHeadToHeadOrchestrated.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
    "BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HCR_hg38.bed",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCR_Hg38.interval_list"
    ],
    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
      "HCR",
      "LCR"
    ]
  },
  "eval_options": null,
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-03-15T18:03:51.605645",
  "created_by": null,
  "finished_at": null
}

CarrotBroadBot avatar Mar 15 '22 18:03 CarrotBroadBot

CARROT test run finished 
 
 {
  "run_id": "ea93cfbf-57fe-4ca6-bf87-78535e66ffb2",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-15 18:03:51.605578569 UTC",
  "status": "evalfailed",
  "test_input": {
    "VariantCallingCarrotOrchestrated.CHM_base_file_name": "CHM113",
    "VariantCallingCarrotOrchestrated.CHM_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.CHM_contamination": 0.0,
    "VariantCallingCarrotOrchestrated.CHM_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm1_chm13_hiseqx_sm_hf3mo.bam",
    "VariantCallingCarrotOrchestrated.CHM_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.NIST_base_file_name": "NA24385",
    "VariantCallingCarrotOrchestrated.NIST_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
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    "VariantCallingCarrotOrchestrated.NIST_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrotOrchestrated.NIST_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.agg_preemptible_tries": 3,
    "VariantCallingCarrotOrchestrated.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrotOrchestrated.contamination": 0.0,
    "VariantCallingCarrotOrchestrated.exome1_base_file_name": "NA12878Exome1",
    "VariantCallingCarrotOrchestrated.exome1_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_calling_regions.v1.interval_list",
    "VariantCallingCarrotOrchestrated.exome1_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram",
    "VariantCallingCarrotOrchestrated.exome1_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram.crai",
    "VariantCallingCarrotOrchestrated.gatk_control_docker": "broadinstitute/gatk-nightly:2022-03-04-4.2.5.0-9-gb097f75c5-NIGHTLY-SNAPSHOT",
    "VariantCallingCarrotOrchestrated.gatk_docker": "image_build:gatk|0a267ad11c3612a61464a84a0ead0d4d89a0ff0b",
    "VariantCallingCarrotOrchestrated.haplotype_scatter_count": 50,
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    "VariantCallingCarrotOrchestrated.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
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    "VariantCallingCarrotOrchestrated.use_gatk3_haplotype_caller": true
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  "test_options": null,
  "eval_input": {
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlLabel": "CONTROLSNAPSHOT2018HG002",
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.CHM_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthLabel": "CHM_GRCh38_SYNDIPv20180222",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz",
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    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.twist_exome.interval_list",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthLabel": "NA12878_GRCh38_TWISTExome",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
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    "BenchmarkVCFsHeadToHeadOrchestrated.hapMap": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkVCFsHeadToHeadOrchestrated.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkVCFsHeadToHeadOrchestrated.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
    "BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HCR_hg38.bed",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCR_Hg38.interval_list"
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    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
      "HCR",
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  },
  "eval_options": null,
  "test_cromwell_job_id": "1d570928-0a94-4b2a-9e05-9fe4e7503d23",
  "eval_cromwell_job_id": "a30cbd5e-1a9e-4a07-badb-f41b0093ec23",
  "created_at": "2022-03-15T18:03:51.605645",
  "created_by": null,
  "finished_at": "2022-03-16T02:01:12.714",
  "results": null
}

CarrotBroadBot avatar Mar 16 '22 02:03 CarrotBroadBot

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Mar 16 '22 14:03 jamesemery

Started a CARROT test run : HaplotypeCaller CARROT Regression Tests_run_2022-03-16 14:19:54.191815405 UTC 
 
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  "run_id": "6353c465-595d-4a96-9f7d-3ea5d54634ca",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-16 14:19:54.191815405 UTC",
  "status": "building",
  "test_input": {
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    "VariantCallingCarrotOrchestrated.CHM_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.CHM_contamination": 0.0,
    "VariantCallingCarrotOrchestrated.CHM_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm1_chm13_hiseqx_sm_hf3mo.bam",
    "VariantCallingCarrotOrchestrated.CHM_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.NIST_base_file_name": "NA24385",
    "VariantCallingCarrotOrchestrated.NIST_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.NIST_contamination": 0.0383312,
    "VariantCallingCarrotOrchestrated.NIST_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrotOrchestrated.NIST_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.agg_preemptible_tries": 3,
    "VariantCallingCarrotOrchestrated.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrotOrchestrated.contamination": 0.0,
    "VariantCallingCarrotOrchestrated.exome1_base_file_name": "NA12878Exome1",
    "VariantCallingCarrotOrchestrated.exome1_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_calling_regions.v1.interval_list",
    "VariantCallingCarrotOrchestrated.exome1_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram",
    "VariantCallingCarrotOrchestrated.exome1_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram.crai",
    "VariantCallingCarrotOrchestrated.gatk_control_docker": "broadinstitute/gatk-nightly:2022-03-04-4.2.5.0-9-gb097f75c5-NIGHTLY-SNAPSHOT",
    "VariantCallingCarrotOrchestrated.gatk_docker": "image_build:gatk|0a267ad11c3612a61464a84a0ead0d4d89a0ff0b",
    "VariantCallingCarrotOrchestrated.haplotype_scatter_count": 50,
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    "VariantCallingCarrotOrchestrated.use_gatk3_haplotype_caller": true
  },
  "test_options": null,
  "eval_input": {
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlLabel": "CONTROLSNAPSHOT2018HG002",
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.CHM_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalLabel": "TESTSNAPSHOT2018HG002",
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.CHM_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthLabel": "CHM_GRCh38_SYNDIPv20180222",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.twist_exome.interval_list",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthLabel": "NA12878_GRCh38_TWISTExome",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.hapMap": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkVCFsHeadToHeadOrchestrated.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkVCFsHeadToHeadOrchestrated.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
    "BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HCR_hg38.bed",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCR_Hg38.interval_list"
    ],
    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
      "HCR",
      "LCR"
    ]
  },
  "eval_options": null,
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-03-16T14:19:54.192086",
  "created_by": null,
  "finished_at": null
}

CarrotBroadBot avatar Mar 16 '22 14:03 CarrotBroadBot

CARROT test run finished 
 
 {
  "run_id": "6353c465-595d-4a96-9f7d-3ea5d54634ca",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-16 14:19:54.191815405 UTC",
  "status": "succeeded",
  "test_input": {
    "VariantCallingCarrotOrchestrated.CHM_base_file_name": "CHM113",
    "VariantCallingCarrotOrchestrated.CHM_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.CHM_contamination": 0.0,
    "VariantCallingCarrotOrchestrated.CHM_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm1_chm13_hiseqx_sm_hf3mo.bam",
    "VariantCallingCarrotOrchestrated.CHM_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.NIST_base_file_name": "NA24385",
    "VariantCallingCarrotOrchestrated.NIST_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
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    "VariantCallingCarrotOrchestrated.NIST_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrotOrchestrated.NIST_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.agg_preemptible_tries": 3,
    "VariantCallingCarrotOrchestrated.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrotOrchestrated.contamination": 0.0,
    "VariantCallingCarrotOrchestrated.exome1_base_file_name": "NA12878Exome1",
    "VariantCallingCarrotOrchestrated.exome1_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_calling_regions.v1.interval_list",
    "VariantCallingCarrotOrchestrated.exome1_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram",
    "VariantCallingCarrotOrchestrated.exome1_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram.crai",
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    "VariantCallingCarrotOrchestrated.gatk_docker": "image_build:gatk|0a267ad11c3612a61464a84a0ead0d4d89a0ff0b",
    "VariantCallingCarrotOrchestrated.haplotype_scatter_count": 50,
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    "VariantCallingCarrotOrchestrated.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
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    "VariantCallingCarrotOrchestrated.use_gatk3_haplotype_caller": true
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  "test_options": null,
  "eval_input": {
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlLabel": "CONTROLSNAPSHOT2018HG002",
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthLabel": "CHM_GRCh38_SYNDIPv20180222",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz",
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    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.twist_exome.interval_list",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthLabel": "NA12878_GRCh38_TWISTExome",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.hapMap": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkVCFsHeadToHeadOrchestrated.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkVCFsHeadToHeadOrchestrated.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
    "BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HCR_hg38.bed",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCR_Hg38.interval_list"
    ],
    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
      "HCR",
      "LCR"
    ]
  },
  "eval_options": null,
  "test_cromwell_job_id": "d6f96a63-9657-4ff6-9934-fe1ab3cea617",
  "eval_cromwell_job_id": "e372bd14-cd1f-4563-8d8a-abf6b6ca7883",
  "created_at": "2022-03-16T14:19:54.192086",
  "created_by": null,
  "finished_at": "2022-03-16T17:26:08.529",
  "results": {
    "CHM controlHCprocesshours": "75.88741944444445",
    "CHM controlHCsystemhours": "0.1663777777777778",
    "CHM controlHCwallclockhours": "52.24009722222222",
    "CHM controlHCwallclockmax": "2.852152777777778",
    "CHM controlMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-CHMSampleHeadToHead/BenchmarkComparison/7ff0db7c-0871-4cda-95f3-fa75436cbb21/call-CONTROLRuntimeTask/cacheCopy/monitoring.pdf",
    "CHM controlindelF1Score": "0.8778",
    "CHM controlindelPrecision": "0.8968",
    "CHM controlsnpF1Score": "0.9813",
    "CHM controlsnpPrecision": "0.9774",
    "CHM controlsnpRecall": "0.9852",
    "CHM controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-CHMSampleHeadToHead/BenchmarkComparison/7ff0db7c-0871-4cda-95f3-fa75436cbb21/call-BenchmarkVCFControlSample/Benchmark/16cd1efe-5cea-403e-8e85-aec15e71bd1d/call-CombineSummaries/summary.csv",
    "CHM evalHCprocesshours": "67.35536666666667",
    "CHM evalHCsystemhours": "0.1557166666666667",
    "CHM evalHCwallclockhours": "42.53388888888889",
    "CHM evalHCwallclockmax": "2.7197444444444443",
    "CHM evalMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-CHMSampleHeadToHead/BenchmarkComparison/7ff0db7c-0871-4cda-95f3-fa75436cbb21/call-EVALRuntimeTask/cacheCopy/monitoring.pdf",
    "CHM evalindelF1Score": "0.8778",
    "CHM evalindelPrecision": "0.8968",
    "CHM evalsnpF1Score": "0.9813",
    "CHM evalsnpPrecision": "0.9774",
    "CHM evalsnpRecall": "0.9852",
    "CHM evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-CHMSampleHeadToHead/BenchmarkComparison/7ff0db7c-0871-4cda-95f3-fa75436cbb21/call-BenchmarkVCFTestSample/Benchmark/2071078a-158e-4c3e-9b2f-907bd501821b/call-CombineSummaries/summary.csv",
    "EXOME1 controlindelF1Score": "0.7573",
    "EXOME1 controlindelPrecision": "0.6882",
    "EXOME1 controlsnpF1Score": "0.9896",
    "EXOME1 controlsnpPrecision": "0.9852",
    "EXOME1 controlsnpRecall": "0.9941",
    "EXOME1 controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-EXOME1SampleHeadToHead/BenchmarkComparison/113b01be-9124-41dd-acc0-5732ef2c7b38/call-BenchmarkVCFControlSample/Benchmark/7222f3cf-155c-423f-bc1e-8194e87ff05f/call-CombineSummaries/summary.csv",
    "EXOME1 evalindelF1Score": "0.7573",
    "EXOME1 evalindelPrecision": "0.6882",
    "EXOME1 evalsnpF1Score": "0.9896",
    "EXOME1 evalsnpPrecision": "0.9852",
    "EXOME1 evalsnpRecall": "0.9941",
    "EXOME1 evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-EXOME1SampleHeadToHead/BenchmarkComparison/113b01be-9124-41dd-acc0-5732ef2c7b38/call-BenchmarkVCFTestSample/Benchmark/e929ad45-5026-4630-8b85-19f6205f068c/call-CombineSummaries/summary.csv",
    "NIST controlHCprocesshours": "90.94291388888888",
    "NIST controlHCsystemhours": "0.182125",
    "NIST controlHCwallclockhours": "63.56370277777778",
    "NIST controlHCwallclockmax": "3.701625",
    "NIST controlMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-NISTSampleHeadToHead/BenchmarkComparison/103cd89c-b177-4a0b-84fc-9553a1f8161f/call-CONTROLRuntimeTask/cacheCopy/monitoring.pdf",
    "NIST controlindelF1Score": "0.9843",
    "NIST controlindelPrecision": "0.9895",
    "NIST controlsnpF1Score": "0.9908",
    "NIST controlsnpPrecision": "0.992",
    "NIST controlsnpRecall": "0.9896",
    "NIST controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-NISTSampleHeadToHead/BenchmarkComparison/103cd89c-b177-4a0b-84fc-9553a1f8161f/call-BenchmarkVCFControlSample/Benchmark/eaf4d582-e197-4e13-8122-5e1ec22591ae/call-CombineSummaries/summary.csv",
    "NIST evalHCprocesshours": "73.06777222222223",
    "NIST evalHCsystemhours": "0.1622555555555555",
    "NIST evalHCwallclockhours": "46.65241388888888",
    "NIST evalHCwallclockmax": "2.7461055555555554",
    "NIST evalMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-NISTSampleHeadToHead/BenchmarkComparison/103cd89c-b177-4a0b-84fc-9553a1f8161f/call-EVALRuntimeTask/cacheCopy/monitoring.pdf",
    "NIST evalindelF1Score": "0.9843",
    "NIST evalindelPrecision": "0.9895",
    "NIST evalsnpF1Score": "0.9908",
    "NIST evalsnpPrecision": "0.992",
    "NIST evalsnpRecall": "0.9896",
    "NIST evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/e372bd14-cd1f-4563-8d8a-abf6b6ca7883/call-NISTSampleHeadToHead/BenchmarkComparison/103cd89c-b177-4a0b-84fc-9553a1f8161f/call-BenchmarkVCFTestSample/Benchmark/87985440-93fa-4a33-ac09-e4cbead32bfb/call-CombineSummaries/summary.csv"
  }
}

CarrotBroadBot avatar Mar 16 '22 17:03 CarrotBroadBot

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Mar 16 '22 18:03 jamesemery

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Mar 16 '22 19:03 jamesemery

Started a CARROT test run : HaplotypeCaller CARROT Regression Tests_run_2022-03-16 19:53:45.833801080 UTC 
 
 {
  "run_id": "8746ca71-df06-4807-9040-5d25e7efb50b",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-16 19:53:45.833801080 UTC",
  "status": "building",
  "test_input": {
    "VariantCallingCarrotOrchestrated.CHM_base_file_name": "CHM113",
    "VariantCallingCarrotOrchestrated.CHM_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.CHM_contamination": 0.0,
    "VariantCallingCarrotOrchestrated.CHM_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm1_chm13_hiseqx_sm_hf3mo.bam",
    "VariantCallingCarrotOrchestrated.CHM_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.NIST_base_file_name": "NA24385",
    "VariantCallingCarrotOrchestrated.NIST_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.NIST_contamination": 0.0383312,
    "VariantCallingCarrotOrchestrated.NIST_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrotOrchestrated.NIST_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrotOrchestrated.agg_preemptible_tries": 3,
    "VariantCallingCarrotOrchestrated.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrotOrchestrated.contamination": 0.0,
    "VariantCallingCarrotOrchestrated.exome1_base_file_name": "NA12878Exome1",
    "VariantCallingCarrotOrchestrated.exome1_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_calling_regions.v1.interval_list",
    "VariantCallingCarrotOrchestrated.exome1_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram",
    "VariantCallingCarrotOrchestrated.exome1_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram.crai",
    "VariantCallingCarrotOrchestrated.gatk_control_docker": "broadinstitute/gatk-nightly:2022-03-04-4.2.5.0-9-gb097f75c5-NIGHTLY-SNAPSHOT",
    "VariantCallingCarrotOrchestrated.gatk_docker": "image_build:gatk|0a267ad11c3612a61464a84a0ead0d4d89a0ff0b",
    "VariantCallingCarrotOrchestrated.haplotype_scatter_count": 50,
    "VariantCallingCarrotOrchestrated.monitoring_script": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/cromwell_monitoring_script.sh",
    "VariantCallingCarrotOrchestrated.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrotOrchestrated.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrotOrchestrated.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrotOrchestrated.use_gatk3_haplotype_caller": true
  },
  "test_options": null,
  "eval_input": {
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.interval_list",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.CHM_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.CHM_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.CHM_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.CHM_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthLabel": "CHM_GRCh38_SYNDIPv20180222",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm.full.m38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.twist_exome.interval_list",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.EXOME1_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcf": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.EXOME1_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthLabel": "NA12878_GRCh38_TWISTExome",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.EXOME1_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/GIAB_v3.3.2_NA12878_hg38.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_control_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_control_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_control_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_control_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalMonitoringExample": "test_output:VariantCallingCarrotOrchestrated.NIST_representative_benchmarking",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf_index",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi",
    "BenchmarkVCFsHeadToHeadOrchestrated.hapMap": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkVCFsHeadToHeadOrchestrated.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkVCFsHeadToHeadOrchestrated.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
    "BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HCR_hg38.bed",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCR_Hg38.interval_list"
    ],
    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
      "HCR",
      "LCR"
    ]
  },
  "eval_options": null,
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-03-16T19:53:45.833854",
  "created_by": null,
  "finished_at": null
}

CarrotBroadBot avatar Mar 16 '22 19:03 CarrotBroadBot

CARROT test run finished 
 
 {
  "run_id": "8746ca71-df06-4807-9040-5d25e7efb50b",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-16 19:53:45.833801080 UTC",
  "status": "succeeded",
  "test_input": {
    "VariantCallingCarrotOrchestrated.CHM_base_file_name": "CHM113",
    "VariantCallingCarrotOrchestrated.CHM_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrotOrchestrated.CHM_contamination": 0.0,
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    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
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    "BenchmarkVCFsHeadToHeadOrchestrated.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
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    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
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      "HCR",
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  "test_cromwell_job_id": "410a88f6-62ca-4745-89fd-df6e30aac65b",
  "eval_cromwell_job_id": "bf86d5b6-04bd-4344-b4fc-8a1df66bb5d9",
  "created_at": "2022-03-16T19:53:45.833854",
  "created_by": null,
  "finished_at": "2022-03-17T00:11:38.702",
  "results": {
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    "CHM controlHCsystemhours": "0.1663777777777778",
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    "NIST evalMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/bf86d5b6-04bd-4344-b4fc-8a1df66bb5d9/call-NISTSampleHeadToHead/BenchmarkComparison/8e62c1c2-cf9c-4530-846e-1e0d6c6d8acf/call-EVALRuntimeTask/cacheCopy/monitoring.pdf",
    "NIST evalindelF1Score": "0.9843",
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    "NIST evalsnpPrecision": "0.992",
    "NIST evalsnpRecall": "0.9896",
    "NIST evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/bf86d5b6-04bd-4344-b4fc-8a1df66bb5d9/call-NISTSampleHeadToHead/BenchmarkComparison/8e62c1c2-cf9c-4530-846e-1e0d6c6d8acf/call-BenchmarkVCFTestSample/Benchmark/d39f91bf-295b-4a15-bd0b-2b7c6b43a347/call-CombineSummaries/summary.csv",
    "ROC_Plots_Reported": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/bf86d5b6-04bd-4344-b4fc-8a1df66bb5d9/call-CreateHTMLReport/report.html"
  }
}

CarrotBroadBot avatar Mar 17 '22 00:03 CarrotBroadBot

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Dec 18 '23 13:12 jamesemery

🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2023-12-18 13:57:17.644566034 UTC

Full details 
 
 {
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  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "run_group_ids": [],
  "name": "HaplotypeCaller CARROT Regression Tests_run_2023-12-18 13:57:17.644566034 UTC",
  "status": "building",
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  "test_wdl_dependencies": null,
  "test_wdl_dependencies_hash": null,
  "eval_wdl": "gs://dsp-methods-carrot-data/wdl-prod/939c8a20-8299-4f22-9735-2fd6b6a8f0d7/eval.wdl",
  "eval_wdl_hash": "48f843a519f65bc9bf17938586ea7b37dc1b81959e200f21cbf98ae3daea13abf2c28daadd3e795e85c49c17b5718d87ccb9bf3921601bebcc7626d1253141a4",
  "eval_wdl_dependencies": null,
  "eval_wdl_dependencies_hash": null,
  "test_input": {
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    "VariantCallingCarrotOrchestrated.CHM_contamination": 0.0,
    "VariantCallingCarrotOrchestrated.CHM_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/chm1_chm13_hiseqx_sm_hf3mo.bam",
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    "VariantCallingCarrotOrchestrated.agg_preemptible_tries": 3,
    "VariantCallingCarrotOrchestrated.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrotOrchestrated.contamination": 0.0,
    "VariantCallingCarrotOrchestrated.exome1_base_file_name": "NA12878Exome1",
    "VariantCallingCarrotOrchestrated.exome1_calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_calling_regions.v1.interval_list",
    "VariantCallingCarrotOrchestrated.exome1_input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram",
    "VariantCallingCarrotOrchestrated.exome1_input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA12878_forPCRplus_1.cram.crai",
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    "VariantCallingCarrotOrchestrated.gatk_docker": "image_build:gatk|0a267ad11c3612a61464a84a0ead0d4d89a0ff0b",
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CarrotBroadBot avatar Dec 18 '23 13:12 CarrotBroadBot

🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: eval_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2023-12-18 13:57:17.644566034 UTC

Full details 
 
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}

CarrotBroadBot avatar Dec 18 '23 18:12 CarrotBroadBot

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Jan 02 '24 16:01 jamesemery

🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-02 16:15:20.291548156 UTC

Full details 
 
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}

CarrotBroadBot avatar Jan 02 '24 16:01 CarrotBroadBot

🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: eval_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-02 16:15:20.291548156 UTC

Full details 
 
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CarrotBroadBot avatar Jan 03 '24 00:01 CarrotBroadBot

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Jan 09 '24 19:01 jamesemery

🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-09 19:30:21.598551444 UTC

Full details 
 
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}

CarrotBroadBot avatar Jan 09 '24 19:01 CarrotBroadBot

🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: eval_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-09 19:30:21.598551444 UTC

Full details 
 
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CarrotBroadBot avatar Jan 10 '24 03:01 CarrotBroadBot

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Jan 17 '24 15:01 jamesemery

🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-17 15:15:22.880396515 UTC

Full details 
 
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CarrotBroadBot avatar Jan 17 '24 15:01 CarrotBroadBot

🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: eval_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-17 15:15:22.880396515 UTC

Full details 
 
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}

CarrotBroadBot avatar Jan 17 '24 22:01 CarrotBroadBot

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Jan 18 '24 17:01 jamesemery

🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-18 17:19:23.444981770 UTC

Full details 
 
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  "name": "HaplotypeCaller CARROT Regression Tests_run_2024-01-18 17:19:23.444981770 UTC",
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}

CarrotBroadBot avatar Jan 18 '24 17:01 CarrotBroadBot

🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: eval_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-18 17:19:23.444981770 UTC

Full details 
 
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  "finished_at": "2024-01-19T01:24:57.261",
  "results": null,
  "errors": null
}

CarrotBroadBot avatar Jan 19 '24 01:01 CarrotBroadBot

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

jamesemery avatar Jan 19 '24 16:01 jamesemery

🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-19 16:18:28.029442655 UTC

Full details 
 
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CarrotBroadBot avatar Jan 19 '24 16:01 CarrotBroadBot

🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: eval_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2024-01-19 16:18:28.029442655 UTC

Full details 
 
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CarrotBroadBot avatar Jan 20 '24 00:01 CarrotBroadBot