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 43s 1m 40s - - 5.3 MB 97% 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 40s 1m 38s - - 6.1 MB 103% 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) 6s 4s - - 6.2 MB 111% 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) 7s 5s - - 6.1 MB 116% 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) 7s 3s - - 3.2 MB 56% 397.4 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 - - 6.1 MB 122% 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) 7s 5s - - 6.1 MB 89% 1.6 MB 432.2 KB 0 bytes 440.0 KB 1
succeeded NFCORE_SAREK:PREPARE_REFERENCE_CNVKIT:CNVKIT_ANTITARGET (intervals) 2m 2s 1m 51s 7s 4s 257.9 MB 378% 117.1 MB 1.4 MB 0 bytes 1.4 MB 1
succeeded NFCORE_SAREK:PREPARE_REFERENCE_CNVKIT:CNVKIT_REFERENCE (Homo_sapiens_assembly38.fasta) 2m 31s 1m 19s 58s 14s 272.1 MB 134% 5.9 GB 10.5 MB 0 bytes 10.5 MB 1
succeeded NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET (input_samplesheet) 1m 28s 1m 27s 0s 0s 0 bytes 109% 77.3 KB 2.9 KB 0 bytes 4.0 KB 1
succeeded NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC (variant_qc_aggregation) 7s 2s 0s 4s 16.9 MB 97% 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) 20m 17s 1m 40s 16m 29s 2m 7s 901.6 MB 226% 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) 15m 5s 1m 40s 11m 49s 1m 35s 839.4 MB 230% 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) 14m 9s 1m 40s 11m 7s 1m 21s 2.1 GB 222% 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) 19m 26s 15s 17m 22s 1m 48s 922.6 MB 211% 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 57s 1m 42s 2m 6s 8s 1.1 GB 111% 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 41s 2s 5m 39s 0s - - - - - - 3
succeeded NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION (869_BIT-N1-BDNA-1_B23H3TCLT3_1) 10s 2s 7s 1s 533.2 MB 220% 97.0 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) 10s 3s 6s 1s 562.6 MB 222% 97.0 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 2s 6s 2s 677.1 MB 227% 97.0 MB 699.2 KB 0 bytes 700.0 KB 1
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