gatk dummy PR for carrot testing **DO NOT MERGE**

Jan 27 '22 18:01 jamesemery

#carrot(GATK HaplotypeCaller Test, VariantCallingCarrot.gatk_docker, )

Jan 27 '22 18:01 jamesemery

CARROT test run finished

 
 {
  "run_id": "847e7d4f-7906-4e81-b34e-b5593784d0b0",
  "test_id": "acce36f4-84fb-4770-b82a-a758dbb79bc8",
  "name": "GATK HaplotypeCaller Test_run_2022-01-27 19:46:31.156656310 UTC",
  "status": "testfailed",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 10,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "eval_input": {
    "Benchmark.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "Benchmark.evalLabel": "TESTSNAPSHOT2018HG002",
    "Benchmark.evalVcf": "test_output:VariantCalling.output_vcf",
    "Benchmark.evalVcfIndex": "test_output:VariantCalling.output_vcf_index",
    "Benchmark.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "Benchmark.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "Benchmark.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "Benchmark.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "Benchmark.referenceVersion": "HG38",
    "Benchmark.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
    ],
    "Benchmark.stratLabels": [
      "exome",
      "LCR"
    ],
    "Benchmark.truthLabel": "HG002_GRCh38_GIAB",
    "Benchmark.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "Benchmark.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": "dbe17be2-3639-40ef-a107-b65193aee07a",
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  "created_at": "2022-01-27T19:46:31.156714",
  "created_by": null,
  "finished_at": "2022-01-28T08:58:14.576",
  "results": null
}

Jan 28 '22 08:01 CarrotBroadBot

#carrot(GATK HaplotypeCaller Test, VariantCallingCarrot.gatk_docker, )

Jan 31 '22 15:01 jamesemery

Started a CARROT test run : GATK HaplotypeCaller Test_run_2022-01-31 15:46:11.708783346 UTC

 
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  "test_id": "acce36f4-84fb-4770-b82a-a758dbb79bc8",
  "name": "GATK HaplotypeCaller Test_run_2022-01-31 15:46:11.708783346 UTC",
  "status": "building",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 10,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "eval_input": {
    "Benchmark.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "Benchmark.evalLabel": "TESTSNAPSHOT2018HG002",
    "Benchmark.evalVcf": "test_output:VariantCalling.output_vcf",
    "Benchmark.evalVcfIndex": "test_output:VariantCalling.output_vcf_index",
    "Benchmark.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "Benchmark.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "Benchmark.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "Benchmark.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "Benchmark.referenceVersion": "HG38",
    "Benchmark.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
    ],
    "Benchmark.stratLabels": [
      "exome",
      "LCR"
    ],
    "Benchmark.truthLabel": "HG002_GRCh38_GIAB",
    "Benchmark.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "Benchmark.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-01-31T15:46:11.708929",
  "created_by": null,
  "finished_at": null
}

Jan 31 '22 15:01 CarrotBroadBot

CARROT test run finished

 
 {
  "run_id": "ca06f9ae-eecd-4168-9abe-50cd10e03db8",
  "test_id": "acce36f4-84fb-4770-b82a-a758dbb79bc8",
  "name": "GATK HaplotypeCaller Test_run_2022-01-31 15:46:11.708783346 UTC",
  "status": "testfailed",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 10,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "eval_input": {
    "Benchmark.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "Benchmark.evalLabel": "TESTSNAPSHOT2018HG002",
    "Benchmark.evalVcf": "test_output:VariantCalling.output_vcf",
    "Benchmark.evalVcfIndex": "test_output:VariantCalling.output_vcf_index",
    "Benchmark.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "Benchmark.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "Benchmark.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "Benchmark.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "Benchmark.referenceVersion": "HG38",
    "Benchmark.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
    ],
    "Benchmark.stratLabels": [
      "exome",
      "LCR"
    ],
    "Benchmark.truthLabel": "HG002_GRCh38_GIAB",
    "Benchmark.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "Benchmark.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": "fa37ab73-c780-43b3-8799-9c9c33791403",
  "eval_cromwell_job_id": null,
  "created_at": "2022-01-31T15:46:11.708929",
  "created_by": null,
  "finished_at": "2022-02-01T05:22:24.782",
  "results": null
}

Feb 01 '22 05:02 CarrotBroadBot

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

Feb 01 '22 19:02 jamesemery

Started a CARROT test run : GATK HaplotypeCaller vs Nightly Test_run_2022-02-01 19:09:10.650558739 UTC

 
 {
  "run_id": "869dc901-0125-41f2-8977-19fbf51bdafd",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-01 19:09:10.650558739 UTC",
  "status": "building",
  "test_input": {
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    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 10,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "eval_input": {
    "BenchmarkComparison.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCalling.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCalling.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCalling.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCalling.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-02-01T19:09:10.650676",
  "created_by": null,
  "finished_at": null
}

Feb 01 '22 19:02 CarrotBroadBot

CARROT test run finished

 
 {
  "run_id": "869dc901-0125-41f2-8977-19fbf51bdafd",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-01 19:09:10.650558739 UTC",
  "status": "testfailed",
  "test_input": {
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    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 10,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "eval_input": {
    "BenchmarkComparison.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCalling.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCalling.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCalling.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCalling.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": "8e99e013-02e9-43f8-84e6-c2910a554eef",
  "eval_cromwell_job_id": null,
  "created_at": "2022-02-01T19:09:10.650676",
  "created_by": null,
  "finished_at": "2022-02-02T06:43:19.685",
  "results": null
}

Feb 02 '22 06:02 CarrotBroadBot

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

Feb 09 '22 15:02 jamesemery

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

Feb 23 '22 19:02 jamesemery

Started a CARROT test run : GATK HaplotypeCaller vs Nightly Test_run_2022-02-23 19:59:31.084286796 UTC

 
 {
  "run_id": "e296eb66-95b2-428a-a31e-3118047b197d",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-23 19:59:31.084286796 UTC",
  "status": "building",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
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    "VariantCallingCarrot.contamination": 0.0383312,
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    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
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    "VariantCallingCarrot.ref_fasta": "gs://emeryj-testing/CarrotData/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://emeryj-testing/CarrotData/Homo_sapiens_assembly38.fasta.fai",
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    "BenchmarkComparison.controlVcf": "test_output:VariantCalling.control_vcf",
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    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
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    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
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    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
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  "created_by": null,
  "finished_at": null
}

Feb 23 '22 19:02 CarrotBroadBot

CARROT test run finished

 
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  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-23 19:59:31.084286796 UTC",
  "status": "testfailed",
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    "VariantCallingCarrot.calling_interval_list": "gs://emeryj-testing/CarrotData/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
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    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://emeryj-testing/CarrotData/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://emeryj-testing/CarrotData/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
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    "VariantCallingCarrot.ref_fasta_index": "gs://emeryj-testing/CarrotData/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
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  "eval_input": {
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    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCalling.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCalling.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCalling.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCalling.output_vcf_index",
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    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
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    "BenchmarkComparison.stratLabels": [
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    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
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  "eval_cromwell_job_id": null,
  "created_at": "2022-02-23T19:59:31.084338",
  "created_by": null,
  "finished_at": "2022-02-23T20:05:18.021",
  "results": null
}

Feb 23 '22 20:02 CarrotBroadBot

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

Feb 23 '22 21:02 jamesemery

Started a CARROT test run : GATK HaplotypeCaller vs Nightly Test_run_2022-02-23 21:13:30.630066805 UTC

 
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  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-23 21:13:30.630066805 UTC",
  "status": "building",
  "test_input": {
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    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
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    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
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    "BenchmarkComparison.controlVcf": "test_output:VariantCalling.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCalling.control_vcf_index",
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    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
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    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
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    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-02-23T21:13:30.630132",
  "created_by": null,
  "finished_at": null
}

Feb 23 '22 21:02 CarrotBroadBot

CARROT test run finished

 
 {
  "run_id": "d1c6dc68-9474-4803-89f3-7e22c52f2fd6",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-23 21:13:30.630066805 UTC",
  "status": "carrotfailed",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "eval_input": {
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    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCalling.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCalling.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCalling.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCalling.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": "4d7d4a30-2d60-4093-939a-5c0eb6ea5486",
  "eval_cromwell_job_id": null,
  "created_at": "2022-02-23T21:13:30.630132",
  "created_by": null,
  "finished_at": "2022-02-24T01:13:28.324278",
  "results": null
}

Feb 24 '22 01:02 CarrotBroadBot

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

Feb 24 '22 15:02 jamesemery

Started a CARROT test run : GATK HaplotypeCaller vs Nightly Test_run_2022-02-24 15:51:30.766998897 UTC

 
 {
  "run_id": "49a3a4ec-c92e-4181-b681-9dd431472165",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-24 15:51:30.766998897 UTC",
  "status": "building",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "eval_input": {
    "BenchmarkComparison.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCallingCarrot.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCallingCarrot.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCallingCarrot.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCallingCarrot.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-02-24T15:51:30.767060",
  "created_by": null,
  "finished_at": null
}

Feb 24 '22 15:02 CarrotBroadBot

CARROT test run finished

 
 {
  "run_id": "49a3a4ec-c92e-4181-b681-9dd431472165",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-24 15:51:30.766998897 UTC",
  "status": "evalfailed",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
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  "eval_input": {
    "BenchmarkComparison.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCallingCarrot.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCallingCarrot.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCallingCarrot.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCallingCarrot.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
      "gs://broad-dsp-spec-ops/scratch/mshand/EvaluationStratIntervalLists/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
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    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": "6c6bbb52-5649-478b-8d95-e50381bcec5f",
  "eval_cromwell_job_id": "d56ac6eb-dab1-48e2-b080-bd5f86a0751b",
  "created_at": "2022-02-24T15:51:30.767060",
  "created_by": null,
  "finished_at": "2022-02-24T16:04:03.018",
  "results": null
}

Feb 24 '22 16:02 CarrotBroadBot

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

Feb 24 '22 19:02 jamesemery

Started a CARROT test run : GATK HaplotypeCaller vs Nightly Test_run_2022-02-24 19:51:30.490690587 UTC

 
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  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-24 19:51:30.490690587 UTC",
  "status": "building",
  "test_input": {
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    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "eval_input": {
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    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCallingCarrot.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCallingCarrot.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCallingCarrot.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCallingCarrot.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_evaluation_regions.v1.interval_list",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-02-24T19:51:30.490746",
  "created_by": null,
  "finished_at": null
}

Feb 24 '22 19:02 CarrotBroadBot

CARROT test run finished

 
 {
  "run_id": "88f12a77-2c28-4def-9ba3-1d88b80f037c",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-02-24 19:51:30.490690587 UTC",
  "status": "succeeded",
  "test_input": {
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    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "eval_input": {
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    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCallingCarrot.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCallingCarrot.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCallingCarrot.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCallingCarrot.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_evaluation_regions.v1.interval_list",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "test_cromwell_job_id": "d7213827-7fd0-4d4d-9a2d-332e6652f625",
  "eval_cromwell_job_id": "c2f81051-c34c-4cf1-a3f5-3f80b78959c2",
  "created_at": "2022-02-24T19:51:30.490746",
  "created_by": null,
  "finished_at": "2022-02-24T23:06:04.523",
  "results": null
}

Feb 24 '22 23:02 CarrotBroadBot

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

Mar 01 '22 18:03 jamesemery

Started a CARROT test run : GATK HaplotypeCaller vs Nightly Test_run_2022-03-01 18:37:45.839345051 UTC

 
 {
  "run_id": "202a0396-1aaa-4fc4-b59e-5f068894e566",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-03-01 18:37:45.839345051 UTC",
  "status": "building",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "test_options": null,
  "eval_input": {
    "BenchmarkComparison.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCallingCarrot.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCallingCarrot.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCallingCarrot.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCallingCarrot.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_evaluation_regions.v1.interval_list",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "eval_options": null,
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-03-01T18:37:45.839419",
  "created_by": null,
  "finished_at": null
}

Mar 01 '22 18:03 CarrotBroadBot

CARROT test run finished

 
 {
  "run_id": "202a0396-1aaa-4fc4-b59e-5f068894e566",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-03-01 18:37:45.839345051 UTC",
  "status": "succeeded",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "test_options": null,
  "eval_input": {
    "BenchmarkComparison.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCallingCarrot.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCallingCarrot.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCallingCarrot.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCallingCarrot.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_evaluation_regions.v1.interval_list",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "eval_options": null,
  "test_cromwell_job_id": "f32b1f78-7094-4a8a-a0f1-fb107184a1c1",
  "eval_cromwell_job_id": "9f7e732d-f92f-4abd-a5e4-32f73e3ab388",
  "created_at": "2022-03-01T18:37:45.839419",
  "created_by": null,
  "finished_at": "2022-03-01T19:14:26.348",
  "results": {
    "control indel f1 score": "0.9903",
    "control indel precision score": "0.9906",
    "control indel recall score": "0.99",
    "control snp f1 score": "0.9901",
    "control snp precision score": "0.989",
    "control snp recall score": "0.9911",
    "indel f1 score": "0.9902",
    "indel precision score": "0.9903",
    "indel recall score": "0.9901",
    "snp f1 score": "0.9899",
    "snp precision score": "0.9887",
    "snp recall score": "0.9911"
  }
}

Mar 01 '22 19:03 CarrotBroadBot

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

Mar 01 '22 22:03 jamesemery

Started a CARROT test run : GATK HaplotypeCaller vs Nightly Test_run_2022-03-01 22:04:38.405022793 UTC

 
 {
  "run_id": "074e8b3b-5149-4e7d-8dcd-0aca2643b625",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-03-01 22:04:38.405022793 UTC",
  "status": "building",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
    "VariantCallingCarrot.input_bam_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bai",
    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "test_options": null,
  "eval_input": {
    "BenchmarkComparison.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCallingCarrot.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCallingCarrot.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCallingCarrot.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCallingCarrot.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_evaluation_regions.v1.interval_list",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "eval_options": null,
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-03-01T22:04:38.405077",
  "created_by": null,
  "finished_at": null
}

Mar 01 '22 22:03 CarrotBroadBot

CARROT test run finished

 
 {
  "run_id": "074e8b3b-5149-4e7d-8dcd-0aca2643b625",
  "test_id": "15973a95-055a-4540-9590-ce40f34411f5",
  "name": "GATK HaplotypeCaller vs Nightly Test_run_2022-03-01 22:04:38.405022793 UTC",
  "status": "succeeded",
  "test_input": {
    "VariantCallingCarrot.agg_preemptible_tries": 3,
    "VariantCallingCarrot.base_file_name": "NA24385",
    "VariantCallingCarrot.break_bands_at_multiples_of": 100000,
    "VariantCallingCarrot.calling_interval_list": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/wgs_calling_regions.hg38.interval_list",
    "VariantCallingCarrot.contamination": 0.0383312,
    "VariantCallingCarrot.final_vcf_base_name": "NA24385",
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "VariantCallingCarrot.haplotype_scatter_count": 50,
    "VariantCallingCarrot.input_bam": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/NA24385_NA24385_O1D1_SM-G947H_v1_NS.bam",
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    "VariantCallingCarrot.ref_dict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "VariantCallingCarrot.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "VariantCallingCarrot.ref_fasta_index": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "VariantCallingCarrot.use_gatk3_haplotype_caller": true
  },
  "test_options": null,
  "eval_input": {
    "BenchmarkComparison.confidenceInterval": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark_noinconsistent.bed",
    "BenchmarkComparison.controlLabel": "CONTROLSNAPSHOT2018HG002",
    "BenchmarkComparison.controlVcf": "test_output:VariantCallingCarrot.control_vcf",
    "BenchmarkComparison.controlVcfIndex": "test_output:VariantCallingCarrot.control_vcf_index",
    "BenchmarkComparison.evalLabel": "TESTSNAPSHOT2018HG002",
    "BenchmarkComparison.evalVcf": "test_output:VariantCallingCarrot.output_vcf",
    "BenchmarkComparison.evalVcfIndex": "test_output:VariantCallingCarrot.output_vcf_index",
    "BenchmarkComparison.hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
    "BenchmarkComparison.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
    "BenchmarkComparison.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkComparison.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkComparison.referenceVersion": "HG38",
    "BenchmarkComparison.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/exome_evaluation_regions.v1.interval_list",
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/LCRFromHengHg38.interval_list"
    ],
    "BenchmarkComparison.stratLabels": [
      "exome",
      "LCR"
    ],
    "BenchmarkComparison.truthLabel": "HG002_GRCh38_GIAB",
    "BenchmarkComparison.truthVcf": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz",
    "BenchmarkComparison.truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HG002_GRCh38_GIAB_1_22_v4.2.1_benchmark.broad-header.vcf.gz.tbi"
  },
  "eval_options": null,
  "test_cromwell_job_id": "e28f2184-ba82-40b1-8b0a-5cf8ddb05449",
  "eval_cromwell_job_id": "2cf6650a-7089-4ef2-9b98-2224afbd3d9c",
  "created_at": "2022-03-01T22:04:38.405077",
  "created_by": null,
  "finished_at": "2022-03-02T04:46:20.806",
  "results": {
    "control indel f1 score": "0.9902",
    "control indel precision score": "0.9903",
    "control indel recall score": "0.9901",
    "control snp f1 score": "0.9899",
    "control snp precision score": "0.9887",
    "control snp recall score": "0.9911",
    "indel f1 score": "0.9902",
    "indel precision score": "0.9903",
    "indel recall score": "0.9901",
    "snp f1 score": "0.9899",
    "snp precision score": "0.9887",
    "snp recall score": "0.9911"
  }
}

Mar 02 '22 04:03 CarrotBroadBot

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

Mar 15 '22 02:03 jamesemery

Started a CARROT test run : HaplotypeCaller CARROT Regression Tests_run_2022-03-15 02:45:40.427499888 UTC

 
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  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-15 02:45:40.427499888 UTC",
  "status": "building",
  "test_input": {
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "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,
    "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.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": "2022-03-15T02:45:40.427752",
  "created_by": null,
  "finished_at": null
}

Mar 15 '22 02:03 CarrotBroadBot

CARROT test run finished

 
 {
  "run_id": "7d96ffaf-77c1-440b-89c0-9cd08a352840",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-03-15 02:45:40.427499888 UTC",
  "status": "testfailed",
  "test_input": {
    "VariantCallingCarrot.gatk_docker": "image_build:gatk|ce0a811376d45c6ea62b40e78abffcd37c0317b4",
    "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",
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  "test_cromwell_job_id": "922f0be2-d538-47f7-991c-f036e6034792",
  "eval_cromwell_job_id": null,
  "created_at": "2022-03-15T02:45:40.427752",
  "created_by": null,
  "finished_at": "2022-03-15T02:46:45.881",
  "results": null
}

Mar 15 '22 02:03 CarrotBroadBot

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dummy PR for carrot testing DO NOT MERGE

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dummy PR for carrot testing **DO NOT MERGE**

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dummy PR for carrot testing DO NOT MERGE