succeeded NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed) 1m 12s 1m 9s - - 5.4 MB 101% 4.6 MB 4.6 MB 0 bytes 4.6 MB 1
succeeded NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity;null) 1m 10s 1m 8s - - 6.2 MB 102% 6.0 MB 1.7 MB 0 bytes 1.7 MB 1
succeeded NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr14_64122012-64122133;null) 4s 3s - - 6.1 MB 91% 1.5 MB 401.1 KB 0 bytes 408.0 KB 1
succeeded NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr1_69091-70008;null) 5s 3s - - 6.1 MB 88% 1.6 MB 442.7 KB 0 bytes 448.0 KB 1
succeeded NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr19_47340800-47341813;null) 4s 3s - - 3.3 MB 56% 396.4 KB 84.1 KB 0 bytes 88.0 KB 1
succeeded NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr4_30730753-30730788;null) 5s 3s - - 6.2 MB 87% 1.4 MB 422.1 KB 0 bytes 428.0 KB 1
succeeded NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr8_93795409-93795507;null) 3s 2s - - 6.1 MB 90% 1.6 MB 432.2 KB 0 bytes 440.0 KB 1
succeeded NFCORE_SAREK:PREPARE_REFERENCE_CNVKIT:CNVKIT_ANTITARGET (intervals) 1m 44s 1m 34s 8s 2s 259.9 MB 408% 117.1 MB 1.4 MB 0 bytes 1.4 MB 1
succeeded NFCORE_SAREK:PREPARE_REFERENCE_CNVKIT:CNVKIT_REFERENCE (Homo_sapiens_assembly38.fasta) 1m 11s 2s 53s 16s 273.7 MB 144% 5.9 GB 10.5 MB 0 bytes 10.5 MB 1
succeeded NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET (input_samplesheet) 1m 11s 1m 10s 0s 0s 0 bytes 100% 78.6 KB 4.4 KB 0 bytes 8.0 KB 1
succeeded NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC (variant_qc_aggregation) 21s 18s 0s 2s 15.2 MB 96% 3.5 MB 19.0 KB 0 bytes 20.0 KB 1
succeeded NFCORE_SAREK:SAREK:AIH_CNV:CalcPanelCoverage (aih_cnv_cohort_calc_panel_coverage_869_BIT) 21m 7s 1m 34s 17m 33s 1m 59s 912.1 MB 224% 401.9 GB 369.0 GB 0 bytes 25.5 GB 1
succeeded NFCORE_SAREK:SAREK:AIH_CNV:CalcPanelCoverage (aih_cnv_cohort_calc_panel_coverage_869_BU7) 16m 19s 1m 19s 13m 10s 1m 49s 826.5 MB 226% 279.3 GB 253.1 GB 0 bytes 17.5 GB 1
succeeded NFCORE_SAREK:SAREK:AIH_CNV:CalcPanelCoverage (aih_cnv_cohort_calc_panel_coverage_869_ELU) 13m 52s 1m 18s 11m 6s 1m 27s 2.1 GB 232% 243.5 GB 220.7 GB 0 bytes 15.3 GB 1
succeeded NFCORE_SAREK:SAREK:AIH_CNV:CalcPanelCoverage (aih_cnv_cohort_calc_panel_coverage_869_WTZ) 20m 6s 16s 17m 41s 2m 8s 3.0 GB 221% 473.8 GB 431.5 GB 160.0 KB 29.9 GB 2
succeeded NFCORE_SAREK:SAREK:AIH_CNV:ClusterPanelRegions (aih_cnv_cohort_cluster_panel_regions) 3m 29s 1m 19s 2m 4s 5s 1.1 GB 105% 218.4 MB 15.4 MB 0 bytes 15.4 MB 1
failed NFCORE_SAREK:SAREK:AIH_CNV:ProcessBatch (aih_cnv_cohort_aih_cnv_process_batch) 5m 51s 2s 5m 49s 0s - - - - - - 3
succeeded NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION (869_BIT-N1-BDNA-1_B23H3TCLT3_1) 10s 3s 7s 0s 445.3 MB 225% 97.1 MB 696.3 KB 0 bytes 700.0 KB 1
succeeded NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION (869_BU7-N1-BDNA-1_B23H3TCLT3_1) 11s 2s 8s 1s 376.3 MB 226% 97.1 MB 698.6 KB 0 bytes 700.0 KB 1
succeeded NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION (869_ELU-N1-BDNA-1_B23H3TCLT3_1) 10s 3s 7s 0s 567.6 MB 247% 97.0 MB 699.2 KB 0 bytes 700.0 KB 1
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