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Support for flow based sequencing #7876

Merged
merged 46 commits into from
Jul 26, 2022
Merged

Support for flow based sequencing #7876

merged 46 commits into from
Jul 26, 2022

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ilyasoifer
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jamesemery
jamesemery reviewed May 31, 2022
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Some minor things that came up that we should check. I notice there is a merge conflict now?

...org/broadinstitute/hellbender/tools/walkers/haplotypecaller/RampedHaplotypeCallerEngine.java
RampUtils.logReads(rpArgs.rampsDebugReads, "onramp: reads before trimming", context.assemblyResult.getRegionForGenotyping().getReads());

RampUtils.logReads(rpArgs.rampsDebugReads, "onramp: BEFORE untrimmedAssemblyResult reads", context.region.getReads());
final AssemblyResultSet untrimmedAssemblyResult = AssemblyBasedCallerUtils.assembleReads(context.region, context.givenAlleles, hcArgs, readsHeader, samplesList, logger, referenceReader, assemblyEngine, aligner,
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context.givenAlleles is outdated here. The forced alleles are handled later, this refers to the forced alleles that might have come from the pileup code.

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Resolved

...in/java/org/broadinstitute/hellbender/engine/filters/flow/WellformedFlowBasedReadFilter.java Outdated
*/
@DocumentedFeature(groupName=HelpConstants.DOC_CAT_READFILTERS,
groupSummary=HelpConstants.DOC_CAT_READFILTERS_SUMMARY,
summary = "Keep only flow based reads that are well-formed"
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please re-add the extradocs here like for the standard wellformed readfilter:

extraDocs = {
                ReadFilterLibrary.ValidAlignmentStartReadFilter.class,
                ReadFilterLibrary.ValidAlignmentEndReadFilter.class,
                AlignmentAgreesWithHeaderReadFilter.class,
                ReadFilterLibrary.HasReadGroupReadFilter.class,
                ReadFilterLibrary.MatchingBasesAndQualsReadFilter.class,
                ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter.class,
                ReadFilterLibrary.SeqIsStoredReadFilter.class,
                ReadFilterLibrary.CigarContainsNoNOperator.class
                }
                ```

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@droazen droazen Jul 15, 2022 •
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This comment from James has not yet been addressed:

please re-add the extradocs here like for the standard wellformed readfilter:

extraDocs = {
                ReadFilterLibrary.ValidAlignmentStartReadFilter.class,
                ReadFilterLibrary.ValidAlignmentEndReadFilter.class,
                AlignmentAgreesWithHeaderReadFilter.class,
                ReadFilterLibrary.HasReadGroupReadFilter.class,
                ReadFilterLibrary.MatchingBasesAndQualsReadFilter.class,
                ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter.class,
                ReadFilterLibrary.SeqIsStoredReadFilter.class,
                ReadFilterLibrary.CigarContainsNoNOperator.class
                }

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Note to self - looks like WellFormedFlowBasedRead is unused. Need to understand

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@ilyasoifer - this filter does have a test, but it was referencing the name of the filter as a string - therefore there was no reference detected by the IDE. Filters invoked by their class name. Resolved by using the class.getSimpleName() instead of the a string. Resolved

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -174,6 +181,13 @@ protected String[] customCommandLineValidation() {
hcArgs.getDragenNameValuePairs(),
HaplotypeCallerArgumentCollection.DRAGEN_GATK_MODE_LONG_NAME);
}
if (hcArgs.flowMode != HaplotypeCallerArgumentCollection.FlowMode.NONE) {
ModeArgumentUtils.setArgValues(
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I notice there is now some extra outputs related to the calling class in the mode argument utils command line output here. Can you fix this?

WARN  ModeArgumentUtils - * The following arguments have had their inputs overwritten:            *
10:34:09.383 WARN  ModeArgumentUtils - * --apply-bqd true (java.io.PrintStream@33359276)                       *
10:34:09.383 WARN  ModeArgumentUtils - * --apply-frd true (java.io.PrintStream@7ca1d70b)

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Fixed

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

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Started a CARROT test run : HaplotypeCaller CARROT Regression Tests_run_2022-06-01 15:19:15.189539495 UTC 
 
 {
  "run_id": "f282b866-8383-4e5e-a4c9-b2ee7929609f",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-06-01 15:19:15.189539495 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|62e5c9ec68fc2cceb0d152453374ed85d49262a9",
    "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": "2022-06-01T15:19:15.189684",
  "created_by": null,
  "finished_at": null
}

@droazen droazen self-requested a review June 1, 2022 15:50
@droazen droazen self-assigned this Jun 1, 2022
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CARROT test run finished 
 
 {
  "run_id": "f282b866-8383-4e5e-a4c9-b2ee7929609f",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-06-01 15:19:15.189539495 UTC",
  "status": "buildfailed",
  "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|62e5c9ec68fc2cceb0d152453374ed85d49262a9",
    "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",
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    "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"
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  },
  "eval_options": null,
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-06-01T15:19:15.189684",
  "created_by": null,
  "finished_at": "2022-06-01T15:58:08.310876",
  "results": null,
  "errors": null
}

@jamesemery
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Collaborator

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

@CarrotBroadBot
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Started a CARROT test run : HaplotypeCaller CARROT Regression Tests_run_2022-06-01 17:59:13.998233683 UTC 
 
 {
  "run_id": "c0f6e7ff-f1ff-484d-9627-2317207526c9",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-06-01 17:59:13.998233683 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",
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    "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|1ce04fd5b2d28ebc198aaad8f84ca77fc32e9ebe",
    "VariantCallingCarrotOrchestrated.haplotype_scatter_count": 50,
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    "VariantCallingCarrotOrchestrated.ref_fasta": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
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    "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",
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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",
    "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",
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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.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": "2022-06-01T17:59:13.998312",
  "created_by": null,
  "finished_at": null
}

@CarrotBroadBot
Copy link

CARROT test run finished 
 
 {
  "run_id": "c0f6e7ff-f1ff-484d-9627-2317207526c9",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-06-01 17:59:13.998233683 UTC",
  "status": "buildfailed",
  "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|1ce04fd5b2d28ebc198aaad8f84ca77fc32e9ebe",
    "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": {
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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",
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    "BenchmarkVCFsHeadToHeadOrchestrated.CHM_evalVcf": "test_output:VariantCallingCarrotOrchestrated.CHM_output_vcf",
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  "results": null,
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}

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gatk-bot commented Jun 1, 2022 •
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Github actions tests reported job failures from actions build 2423439288
Failures in the following jobs:

Test Type JDK Job ID Logs
integration 11 2423439288.12 logs
variantcalling 8 2423439288.2 logs
integration 8 2423439288.0 logs

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gatk-bot commented Jun 1, 2022

Github actions tests reported job failures from actions build 2423963023
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling 8 2423963023.2 logs

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gatk-bot commented Jun 2, 2022

Github actions tests reported job failures from actions build 2426277785
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling 8 2426277785.2 logs

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codecov bot commented Jun 2, 2022 •
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Codecov Report

Merging #7876 (825a63f) into master (5f9f12b) will decrease coverage by 0.374%.
The diff coverage is 76.106%.

@@               Coverage Diff               @@
##              master     #7876       +/-   ##
===============================================
- Coverage     87.063%   86.689%   -0.374%     
- Complexity     37008     38399     +1391     
===============================================
  Files           2218      2308       +90     
  Lines         173760    180119     +6359     
  Branches       18770     19822     +1052     
===============================================
+ Hits          151281    156143     +4862     
- Misses         15895     17036     +1141     
- Partials        6584      6940      +356
Impacted Files Coverage Δ
...ine/GATKPlugin/GATKAnnotationPluginDescriptor.java 78.947% <0.000%> (-4.904%) ⬇️
...nstitute/hellbender/engine/filters/ReadFilter.java 83.784% <0.000%> (-16.216%) ⬇️
...stitute/hellbender/tools/HaplotypeCallerSpark.java 66.667% <ø> (ø)
...ender/tools/walkers/annotator/AnnotationUtils.java 90.476% <ø> (ø)
...r/tools/walkers/annotator/JumboInfoAnnotation.java 100.000% <ø> (ø)
...er/tools/walkers/annotator/StrandBiasBySample.java 72.000% <0.000%> (-6.261%) ⬇️
...ers/genotyper/IndependentSampleGenotypesModel.java 93.548% <ø> (ø)
...kers/groundtruth/LocationTranslationException.java 0.000% <0.000%> (ø)
...walkers/haplotypecaller/AssemblyRegionTrimmer.java 43.750% <0.000%> (-0.461%) ⬇️
...allerReadThreadingAssemblerArgumentCollection.java 62.500% <ø> (ø)
... and 207 more

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gatk-bot commented Jun 2, 2022

Github actions tests reported job failures from actions build 2430257415
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling 8 2430257415.2 logs

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gatk-bot commented Jun 6, 2022 •
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Github actions tests reported job failures from actions build 2450316352
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling 8 2450316352.2 logs
variantcalling 8 2450316352.2 logs

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gatk-bot commented Jun 8, 2022

Github actions tests reported job failures from actions build 2462193805
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling 8 2462193805.2 logs

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gatk-bot commented Jun 9, 2022

Github actions tests reported job failures from actions build 2468879043
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling 8 2468879043.2 logs

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Github actions tests reported job failures from actions build 2475473068
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling 8 2475473068.2 logs

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Github actions tests reported job failures from actions build 2476740972
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling 8 2476740972.2 logs

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

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🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2022-06-13 20:49:22.040601374 UTC

Full details 
 
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}

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

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🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2022-06-13 20:50:21.938874311 UTC

Full details 
 
 {
  "run_id": "85b43c98-aca0-4f9c-b56b-f4d3c29b84da",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-06-13 20:50:21.938874311 UTC",
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  "created_at": "2022-06-13T20:50:21.938934",
  "created_by": null,
  "finished_at": null
}

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🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: build_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2022-06-13 20:49:22.040601374 UTC

Full details 
 
 {
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  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-06-13 20:49:22.040601374 UTC",
  "status": "buildfailed",
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  "created_at": "2022-06-13T20:49:22.040855",
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  "finished_at": "2022-06-13T21:28:19.122154",
  "results": null,
  "errors": null
}

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🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: build_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2022-06-13 20:50:21.938874311 UTC

Full details 
 
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  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-06-13 20:50:21.938874311 UTC",
  "status": "buildfailed",
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  "finished_at": "2022-06-13T21:28:19.925729",
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}

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

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🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2022-06-14 16:42:21.893638546 UTC

Full details 
 
 {
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  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-06-14 16:42:21.893638546 UTC",
  "status": "building",
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    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalLabel": "TESTSNAPSHOT2018HG002",
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    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalRuntimeSummaries": "test_output:VariantCallingCarrotOrchestrated.NIST_output_runtimes",
    "BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf",
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  "created_at": "2022-06-14T16:42:21.893697",
  "created_by": null,
  "finished_at": null
}

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🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: build_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2022-06-14 16:42:21.893638546 UTC

Full details 
 
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  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-06-14 16:42:21.893638546 UTC",
  "status": "buildfailed",
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  "created_by": null,
  "finished_at": "2022-06-14T17:12:19.188417",
  "results": null,
  "errors": null
}

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Github actions tests reported job failures from actions build 2504794730
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling 8 2504794730.2 logs

dror27 and others added 6 commits July 22, 2022 12:47
@dror27 @jamesemery
DK PR Changes
4b29a5f 
NonRandomReplacementMode test added

nonRandomDownsamplingMode turned into override method

PartialReadWalker example and test added

FlowBasedTPAttributeSymetricReadFilter unit test

CalculateAverageCombinedAnnotations included in command line

FlowBasedAlignmentArgumentCollection moved

getFlowMatrixModsInstructions moved to utils class

remove use of explicit string

FlowAnnotatorUnitTest extends GATKBaseTest

new flow annotation doc

dragen and flow mode are mutually exclusive

string literal removed
@ilyasoifer @jamesemery
PR comments
862bbe7
@ilyasoifer @jamesemery
PR comments
d3c7cf4
@meganshand @jamesemery
adding documentation for RawGtCount
e8926ea
@jamesemery
removed cloudbuild.yml
cc670d2
@jamesemery
resolving various issues from the code review comments
1c8d481
@jamesemery
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#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

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🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2022-07-22 17:02:00.286469813 UTC

Full details 
 
 {
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  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-07-22 17:02:00.286469813 UTC",
  "status": "building",
  "test_input": {
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  "created_at": "2022-07-22T17:02:00.286664",
  "created_by": null,
  "finished_at": null
}

@CarrotBroadBot
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🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: build_failed

Run: HaplotypeCaller CARROT Regression Tests_run_2022-07-22 17:02:00.286469813 UTC

Full details 
 
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  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-07-22 17:02:00.286469813 UTC",
  "status": "buildfailed",
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  "finished_at": "2022-07-22T17:17:56.932848",
  "results": null,
  "errors": null
}

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

@CarrotBroadBot
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🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2022-07-22 17:23:11.546909540 UTC

Full details 
 
 {
  "run_id": "3d572c63-96eb-4429-98da-e698e4540893",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-07-22 17:23:11.546909540 UTC",
  "status": "building",
  "test_input": {
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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",
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    "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",
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    "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",
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    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
    "BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
      "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/HCR_hg38.bed",
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    ],
    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
      "HCR",
      "LCR"
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  },
  "eval_options": null,
  "test_cromwell_job_id": null,
  "eval_cromwell_job_id": null,
  "created_at": "2022-07-22T17:23:11.546971",
  "created_by": null,
  "finished_at": null
}

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gatk-bot commented Jul 22, 2022 •
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Github actions tests reported job failures from actions build 2720043735
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud 8 2720043735.10 logs
cloud 11 2720043735.11 logs
integration 11 2720043735.12 logs

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gatk-bot commented Jul 22, 2022 •
edited
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Github actions tests reported job failures from actions build 2720146764
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud 8 2720146764.10 logs
cloud 11 2720146764.11 logs
integration 11 2720146764.12 logs
integration 8 2720146764.0 logs

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🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: succeeded

Run: HaplotypeCaller CARROT Regression Tests_run_2022-07-22 17:23:11.546909540 UTC

Results
Results
CHM controlHCprocesshours 75.88741944444445
CHM controlHCsystemhours 0.1663777777777778
CHM controlHCwallclockhours 52.24009722222222
CHM controlHCwallclockmax 2.852152777777778
CHM controlMonitoringLogs View in the GCS Console
CHM controlindelF1Score 0.8724
CHM controlindelPrecision 0.8814
CHM controlsnpF1Score 0.9784
CHM controlsnpPrecision 0.9706
CHM controlsnpRecall 0.9863
CHM controlsummary View in the GCS Console
CHM evalHCprocesshours 78.99195555555558
CHM evalHCsystemhours 0.16168333333333337
CHM evalHCwallclockhours 55.43875833333334
CHM evalHCwallclockmax 2.913311111111111
CHM evalMonitoringLogs View in the GCS Console
CHM evalindelF1Score 0.8724
CHM evalindelPrecision 0.8814
CHM evalsnpF1Score 0.9784
CHM evalsnpPrecision 0.9706
CHM evalsnpRecall 0.9863
CHM evalsummary View in the GCS Console
EXOME1 controlindelF1Score 0.727
EXOME1 controlindelPrecision 0.632
EXOME1 controlsnpF1Score 0.9878
EXOME1 controlsnpPrecision 0.9815
EXOME1 controlsnpRecall 0.9941
EXOME1 controlsummary View in the GCS Console
EXOME1 evalindelF1Score 0.727
EXOME1 evalindelPrecision 0.632
EXOME1 evalsnpF1Score 0.9878
EXOME1 evalsnpPrecision 0.9815
EXOME1 evalsnpRecall 0.9941
EXOME1 evalsummary View in the GCS Console
NIST controlHCprocesshours 90.94291388888888
NIST controlHCsystemhours 0.182125
NIST controlHCwallclockhours 63.56370277777778
NIST controlHCwallclockmax 3.701625
NIST controlMonitoringLogs View in the GCS Console
NIST controlindelF1Score 0.9902
NIST controlindelPrecision 0.9903
NIST controlsnpF1Score 0.9899
NIST controlsnpPrecision 0.9887
NIST controlsnpRecall 0.9911
NIST controlsummary View in the GCS Console
NIST evalHCprocesshours 92.82975
NIST evalHCsystemhours 0.17177777777777778
NIST evalHCwallclockhours 66.4404388888889
NIST evalHCwallclockmax 3.325327777777778
NIST evalMonitoringLogs View in the GCS Console
NIST evalindelF1Score 0.9902
NIST evalindelPrecision 0.9903
NIST evalsnpF1Score 0.9899
NIST evalsnpPrecision 0.9887
NIST evalsnpRecall 0.9911
NIST evalsummary View in the GCS Console
ROC_Plots_Reported View in the GCS Console
Full details 
 
 {
  "run_id": "3d572c63-96eb-4429-98da-e698e4540893",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-07-22 17:23:11.546909540 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",
    "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|cd5bd81424bd6a0b7afd11178d3182d6328ceae1",
    "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"
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  },
  "eval_options": null,
  "test_cromwell_job_id": "07271d7b-729d-4db9-862d-5f992a60a598",
  "eval_cromwell_job_id": "89508d5f-29f1-4534-9fe1-220a80de17c4",
  "created_at": "2022-07-22T17:23:11.546971",
  "created_by": null,
  "finished_at": "2022-07-23T02:09:23.327",
  "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/89508d5f-29f1-4534-9fe1-220a80de17c4/call-CHMSampleHeadToHead/BenchmarkComparison/a2a2515a-b32a-44a6-a6d1-9a6d0d2199bb/call-CONTROLRuntimeTask/cacheCopy/monitoring.pdf",
    "CHM controlindelF1Score": "0.8724",
    "CHM controlindelPrecision": "0.8814",
    "CHM controlsnpF1Score": "0.9784",
    "CHM controlsnpPrecision": "0.9706",
    "CHM controlsnpRecall": "0.9863",
    "CHM controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/89508d5f-29f1-4534-9fe1-220a80de17c4/call-CHMSampleHeadToHead/BenchmarkComparison/a2a2515a-b32a-44a6-a6d1-9a6d0d2199bb/call-BenchmarkVCFControlSample/Benchmark/2c4ad666-e885-4e23-bd5c-d54ca521ffbf/call-CombineSummaries/summary.csv",
    "CHM evalHCprocesshours": "78.99195555555558",
    "CHM evalHCsystemhours": "0.16168333333333337",
    "CHM evalHCwallclockhours": "55.43875833333334",
    "CHM evalHCwallclockmax": "2.913311111111111",
    "CHM evalMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/89508d5f-29f1-4534-9fe1-220a80de17c4/call-CHMSampleHeadToHead/BenchmarkComparison/a2a2515a-b32a-44a6-a6d1-9a6d0d2199bb/call-EVALRuntimeTask/monitoring.pdf",
    "CHM evalindelF1Score": "0.8724",
    "CHM evalindelPrecision": "0.8814",
    "CHM evalsnpF1Score": "0.9784",
    "CHM evalsnpPrecision": "0.9706",
    "CHM evalsnpRecall": "0.9863",
    "CHM evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/89508d5f-29f1-4534-9fe1-220a80de17c4/call-CHMSampleHeadToHead/BenchmarkComparison/a2a2515a-b32a-44a6-a6d1-9a6d0d2199bb/call-BenchmarkVCFTestSample/Benchmark/76484c8b-d024-45b4-b1e0-2ff2b9adf2c0/call-CombineSummaries/summary.csv",
    "EXOME1 controlindelF1Score": "0.727",
    "EXOME1 controlindelPrecision": "0.632",
    "EXOME1 controlsnpF1Score": "0.9878",
    "EXOME1 controlsnpPrecision": "0.9815",
    "EXOME1 controlsnpRecall": "0.9941",
    "EXOME1 controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/89508d5f-29f1-4534-9fe1-220a80de17c4/call-EXOME1SampleHeadToHead/BenchmarkComparison/1269d993-e13f-4635-a12a-e65fdaa4ed16/call-BenchmarkVCFControlSample/Benchmark/492b823a-1e34-46cd-b842-5f042bb31ee8/call-CombineSummaries/summary.csv",
    "EXOME1 evalindelF1Score": "0.727",
    "EXOME1 evalindelPrecision": "0.632",
    "EXOME1 evalsnpF1Score": "0.9878",
    "EXOME1 evalsnpPrecision": "0.9815",
    "EXOME1 evalsnpRecall": "0.9941",
    "EXOME1 evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/89508d5f-29f1-4534-9fe1-220a80de17c4/call-EXOME1SampleHeadToHead/BenchmarkComparison/1269d993-e13f-4635-a12a-e65fdaa4ed16/call-BenchmarkVCFTestSample/Benchmark/834b6562-65d7-4daf-857a-d9118a6456b7/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/89508d5f-29f1-4534-9fe1-220a80de17c4/call-NISTSampleHeadToHead/BenchmarkComparison/338d644e-3327-471e-9d17-1c103fa5e01e/call-CONTROLRuntimeTask/cacheCopy/monitoring.pdf",
    "NIST controlindelF1Score": "0.9902",
    "NIST controlindelPrecision": "0.9903",
    "NIST controlsnpF1Score": "0.9899",
    "NIST controlsnpPrecision": "0.9887",
    "NIST controlsnpRecall": "0.9911",
    "NIST controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/89508d5f-29f1-4534-9fe1-220a80de17c4/call-NISTSampleHeadToHead/BenchmarkComparison/338d644e-3327-471e-9d17-1c103fa5e01e/call-BenchmarkVCFControlSample/Benchmark/145d88de-5810-47e1-972a-18ff0169fe27/call-CombineSummaries/summary.csv",
    "NIST evalHCprocesshours": "92.82975",
    "NIST evalHCsystemhours": "0.17177777777777778",
    "NIST evalHCwallclockhours": "66.4404388888889",
    "NIST evalHCwallclockmax": "3.325327777777778",
    "NIST evalMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/89508d5f-29f1-4534-9fe1-220a80de17c4/call-NISTSampleHeadToHead/BenchmarkComparison/338d644e-3327-471e-9d17-1c103fa5e01e/call-EVALRuntimeTask/monitoring.pdf",
    "NIST evalindelF1Score": "0.9902",
    "NIST evalindelPrecision": "0.9903",
    "NIST evalsnpF1Score": "0.9899",
    "NIST evalsnpPrecision": "0.9887",
    "NIST evalsnpRecall": "0.9911",
    "NIST evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/89508d5f-29f1-4534-9fe1-220a80de17c4/call-NISTSampleHeadToHead/BenchmarkComparison/338d644e-3327-471e-9d17-1c103fa5e01e/call-BenchmarkVCFTestSample/Benchmark/e37c2b01-a62d-4b8c-9fb3-6f86d8377ca7/call-CombineSummaries/summary.csv",
    "ROC_Plots_Reported": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/89508d5f-29f1-4534-9fe1-220a80de17c4/call-CreateHTMLReport/cacheCopy/report.html"
  },
  "errors": null
}

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🥕CARROT🥕 run report stub finished

for run HaplotypeCaller CARROT Regression Tests_run_2022-07-22 17:23:11.546909540 UTC (3d572c63-96eb-4429-98da-e698e4540893)

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empty_notebook View in the GCS Console
html_report View in the GCS Console
populated_notebook View in the GCS Console
run_csv_zip View in the GCS Console

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

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🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2022-07-25 15:10:00.795026401 UTC

Full details 
 
 {
  "run_id": "e8a17046-7dac-497d-9a1c-217251f75d96",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-07-25 15:10:00.795026401 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|825a63f15ea4deb6fbfc1db6ea5148d0d23faded",
    "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": "2022-07-25T15:10:00.795227",
  "created_by": null,
  "finished_at": null
}

droazen
droazen approved these changes Jul 25, 2022
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Looks like all review comments have been addressed and tests are now passing!

@jamesemery Go ahead and squash/merge as soon as the Carrot tests pass a final time. Be sure to write a nice commit message for the release notes with a high-level description of the features added here.

@ilyasoifer Will you be restoring the reverted BQSR changes in a future PR? Are they needed by your current pipeline?

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🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: succeeded

Run: HaplotypeCaller CARROT Regression Tests_run_2022-07-25 15:10:00.795026401 UTC

Results
Results
CHM controlHCprocesshours 75.88741944444445
CHM controlHCsystemhours 0.1663777777777778
CHM controlHCwallclockhours 52.24009722222222
CHM controlHCwallclockmax 2.852152777777778
CHM controlMonitoringLogs View in the GCS Console
CHM controlindelF1Score 0.8724
CHM controlindelPrecision 0.8814
CHM controlsnpF1Score 0.9784
CHM controlsnpPrecision 0.9706
CHM controlsnpRecall 0.9863
CHM controlsummary View in the GCS Console
CHM evalHCprocesshours 78.10181666666668
CHM evalHCsystemhours 0.16157500000000005
CHM evalHCwallclockhours 55.006172222222226
CHM evalHCwallclockmax 2.8554194444444443
CHM evalMonitoringLogs View in the GCS Console
CHM evalindelF1Score 0.8724
CHM evalindelPrecision 0.8814
CHM evalsnpF1Score 0.9784
CHM evalsnpPrecision 0.9706
CHM evalsnpRecall 0.9863
CHM evalsummary View in the GCS Console
EXOME1 controlindelF1Score 0.727
EXOME1 controlindelPrecision 0.632
EXOME1 controlsnpF1Score 0.9878
EXOME1 controlsnpPrecision 0.9815
EXOME1 controlsnpRecall 0.9941
EXOME1 controlsummary View in the GCS Console
EXOME1 evalindelF1Score 0.727
EXOME1 evalindelPrecision 0.632
EXOME1 evalsnpF1Score 0.9878
EXOME1 evalsnpPrecision 0.9815
EXOME1 evalsnpRecall 0.9941
EXOME1 evalsummary View in the GCS Console
NIST controlHCprocesshours 90.94291388888888
NIST controlHCsystemhours 0.182125
NIST controlHCwallclockhours 63.56370277777778
NIST controlHCwallclockmax 3.701625
NIST controlMonitoringLogs View in the GCS Console
NIST controlindelF1Score 0.9902
NIST controlindelPrecision 0.9903
NIST controlsnpF1Score 0.9899
NIST controlsnpPrecision 0.9887
NIST controlsnpRecall 0.9911
NIST controlsummary View in the GCS Console
NIST evalHCprocesshours 95.03499722222222
NIST evalHCsystemhours 0.17304166666666665
NIST evalHCwallclockhours 67.81165555555557
NIST evalHCwallclockmax 3.691061111111111
NIST evalMonitoringLogs View in the GCS Console
NIST evalindelF1Score 0.9902
NIST evalindelPrecision 0.9903
NIST evalsnpF1Score 0.9899
NIST evalsnpPrecision 0.9887
NIST evalsnpRecall 0.9911
NIST evalsummary View in the GCS Console
ROC_Plots_Reported View in the GCS Console
Full details 
 
 {
  "run_id": "e8a17046-7dac-497d-9a1c-217251f75d96",
  "test_id": "c3de522b-7ce5-4a51-8b57-1cea628dd93a",
  "name": "HaplotypeCaller CARROT Regression Tests_run_2022-07-25 15:10:00.795026401 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",
    "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",
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    "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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    ],
    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
      "HCR",
      "LCR"
    ]
  },
  "eval_options": null,
  "test_cromwell_job_id": "a8ee297d-9fd6-433f-ac22-14488a09b832",
  "eval_cromwell_job_id": "2a8ce326-baa5-4052-bff9-bd684393ff6c",
  "created_at": "2022-07-25T15:10:00.795227",
  "created_by": null,
  "finished_at": "2022-07-26T00:11:26.646",
  "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/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-CHMSampleHeadToHead/BenchmarkComparison/a1db35b8-cc7b-4019-bdd0-9f423762542e/call-CONTROLRuntimeTask/cacheCopy/monitoring.pdf",
    "CHM controlindelF1Score": "0.8724",
    "CHM controlindelPrecision": "0.8814",
    "CHM controlsnpF1Score": "0.9784",
    "CHM controlsnpPrecision": "0.9706",
    "CHM controlsnpRecall": "0.9863",
    "CHM controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-CHMSampleHeadToHead/BenchmarkComparison/a1db35b8-cc7b-4019-bdd0-9f423762542e/call-BenchmarkVCFControlSample/Benchmark/7195c554-534f-43ef-80c2-77bdafa1827f/call-CombineSummaries/summary.csv",
    "CHM evalHCprocesshours": "78.10181666666668",
    "CHM evalHCsystemhours": "0.16157500000000005",
    "CHM evalHCwallclockhours": "55.006172222222226",
    "CHM evalHCwallclockmax": "2.8554194444444443",
    "CHM evalMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-CHMSampleHeadToHead/BenchmarkComparison/a1db35b8-cc7b-4019-bdd0-9f423762542e/call-EVALRuntimeTask/monitoring.pdf",
    "CHM evalindelF1Score": "0.8724",
    "CHM evalindelPrecision": "0.8814",
    "CHM evalsnpF1Score": "0.9784",
    "CHM evalsnpPrecision": "0.9706",
    "CHM evalsnpRecall": "0.9863",
    "CHM evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-CHMSampleHeadToHead/BenchmarkComparison/a1db35b8-cc7b-4019-bdd0-9f423762542e/call-BenchmarkVCFTestSample/Benchmark/5c4f9069-86b3-4d8c-b765-38a67169e4b4/call-CombineSummaries/summary.csv",
    "EXOME1 controlindelF1Score": "0.727",
    "EXOME1 controlindelPrecision": "0.632",
    "EXOME1 controlsnpF1Score": "0.9878",
    "EXOME1 controlsnpPrecision": "0.9815",
    "EXOME1 controlsnpRecall": "0.9941",
    "EXOME1 controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-EXOME1SampleHeadToHead/BenchmarkComparison/688ca200-89b9-479b-b701-5fa0b0854778/call-BenchmarkVCFControlSample/Benchmark/59d8f8b1-1323-4e56-a1b1-0b1b2c8f2cc0/call-CombineSummaries/summary.csv",
    "EXOME1 evalindelF1Score": "0.727",
    "EXOME1 evalindelPrecision": "0.632",
    "EXOME1 evalsnpF1Score": "0.9878",
    "EXOME1 evalsnpPrecision": "0.9815",
    "EXOME1 evalsnpRecall": "0.9941",
    "EXOME1 evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-EXOME1SampleHeadToHead/BenchmarkComparison/688ca200-89b9-479b-b701-5fa0b0854778/call-BenchmarkVCFTestSample/Benchmark/1b8ccc58-1ead-4443-b6a8-64f767abfc70/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/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-NISTSampleHeadToHead/BenchmarkComparison/d1047505-b7bc-455d-851f-fbed8d81e895/call-CONTROLRuntimeTask/cacheCopy/monitoring.pdf",
    "NIST controlindelF1Score": "0.9902",
    "NIST controlindelPrecision": "0.9903",
    "NIST controlsnpF1Score": "0.9899",
    "NIST controlsnpPrecision": "0.9887",
    "NIST controlsnpRecall": "0.9911",
    "NIST controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-NISTSampleHeadToHead/BenchmarkComparison/d1047505-b7bc-455d-851f-fbed8d81e895/call-BenchmarkVCFControlSample/Benchmark/5388d7b6-6bcd-451d-9a4e-925b386ecd0c/call-CombineSummaries/summary.csv",
    "NIST evalHCprocesshours": "95.03499722222222",
    "NIST evalHCsystemhours": "0.17304166666666665",
    "NIST evalHCwallclockhours": "67.81165555555557",
    "NIST evalHCwallclockmax": "3.691061111111111",
    "NIST evalMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-NISTSampleHeadToHead/BenchmarkComparison/d1047505-b7bc-455d-851f-fbed8d81e895/call-EVALRuntimeTask/monitoring.pdf",
    "NIST evalindelF1Score": "0.9902",
    "NIST evalindelPrecision": "0.9903",
    "NIST evalsnpF1Score": "0.9899",
    "NIST evalsnpPrecision": "0.9887",
    "NIST evalsnpRecall": "0.9911",
    "NIST evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-NISTSampleHeadToHead/BenchmarkComparison/d1047505-b7bc-455d-851f-fbed8d81e895/call-BenchmarkVCFTestSample/Benchmark/faae76f3-8378-4271-9822-5d2587113415/call-CombineSummaries/summary.csv",
    "ROC_Plots_Reported": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/2a8ce326-baa5-4052-bff9-bd684393ff6c/call-CreateHTMLReport/cacheCopy/report.html"
  },
  "errors": null
}

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🥕CARROT🥕 run report stub finished

for run HaplotypeCaller CARROT Regression Tests_run_2022-07-25 15:10:00.795026401 UTC (e8a17046-7dac-497d-9a1c-217251f75d96)

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@jamesemery jamesemery merged commit f1e7265 into master Jul 26, 2022
@jamesemery jamesemery deleted the UG_feature_branch branch July 26, 2022 13:38
@meganshand meganshand restored the UG_feature_branch branch October 28, 2022 13:52
@meganshand meganshand deleted the UG_feature_branch branch October 28, 2022 13:53
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@droazen droazen droazen approved these changes

@meganshand meganshand Awaiting requested review from meganshand

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