succeeded NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr9_114918096-114918138) 4s 2s - - 6.2 MB 104% 619.7 KB 150.5 KB 0 bytes 156.0 KB 1
succeeded NFCORE_SAREK:PREPARE_REFERENCE_CNVKIT:CNVKIT_ANTITARGET (intervals) 1m 10s 1m 1s 8s 1s 260.0 MB 203% 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 8s 4s 55s 9s 274.4 MB 114% 5.9 GB 10.5 MB 0 bytes 10.5 MB 1
succeeded NFCORE_SAREK:PUBLISH_INPUT_SAMPLESHEET (input_samplesheet) 6s 5s 0s 0s 0 bytes 115% 109.3 KB 794 bytes 0 bytes 4.0 KB 4
succeeded NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC (variant_qc_aggregation) 18s 16s 0s 1s 15.1 MB 108% 2.7 MB 5.7 KB 0 bytes 12.0 KB 2
succeeded NFCORE_SAREK:SAREK:BAM_APPLYBQSR_SENTIEON:SAMTOOLS_INDEX (1029_BGFD-N1-BDNA-1_2375WFLT3_s30) 2m 57s 4s 1m 59s 54s 15.8 MB 135% 24.5 GB 2.8 MB 24.5 GB 2.8 MB 3
succeeded NFCORE_SAREK:SAREK:BAM_APPLYBQSR_SENTIEON:SAMTOOLS_INDEX (1029_BGFD-T1-TDNA-1_23FC2GLT4_s30) 14m 57s 2s 10m 10s 4m 45s 36.7 MB 124% 129.1 GB 3.4 MB 129.1 GB 3.4 MB 3
succeeded NFCORE_SAREK:SAREK:BAM_APPLYBQSR_SENTIEON:SENTIEON_QUALCAL (1029_BGFD-N1-BDNA-1_2375WFLT3_s30) 9m 50s 4s 8m 6s 1m 39s 1.6 GB 1168% 41.2 GB 49.2 GB 0 bytes 49.2 GB 3
succeeded NFCORE_SAREK:SAREK:BAM_APPLYBQSR_SENTIEON:SENTIEON_QUALCAL (1029_BGFD-T1-TDNA-1_23FC2GLT4_s30) 36m 22s 4s 27m 26s 8m 51s 3.5 GB 1179% 200.1 GB 258.2 GB 70.4 GB 258.2 GB 3
succeeded NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR_SENTIEON:SENTIEON_QUALCAL (1029_BGFD-N1-BDNA-1_2375WFLT3_s30) 3m 46s 59s 1m 41s 1m 5s 1.3 GB 1161% 16.3 GB 31.8 MB 0 bytes 31.8 MB 2
succeeded NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR_SENTIEON:SENTIEON_QUALCAL (1029_BGFD-T1-TDNA-1_23FC2GLT4_s30) 15m 43s 59s 9m 20s 5m 23s 2.5 GB 1153% 70.7 GB 28.6 MB 70.3 GB 28.5 MB 2
succeeded NFCORE_SAREK:SAREK:BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION (1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30) 15m 8s 1m 51s 13m 14s 2s 108.7 MB 105% 271.3 MB 1003 bytes 0 bytes 8.0 KB 3
succeeded NFCORE_SAREK:SAREK:BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP (1029_BGFD-N1-BDNA-1_2375WFLT3_s30) 3m 10s 33s 1m 15s 1m 21s 483.9 MB 111% 5.9 GB 54.9 MB 10.5 GB 54.9 MB 3
succeeded NFCORE_SAREK:SAREK:BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP (1029_BGFD-T1-TDNA-1_23FC2GLT4_s30) 9m 53s 40s 4m 28s 4m 44s 558.9 MB 106% 24.6 GB 193.0 MB 44.3 GB 193.5 MB 3
succeeded NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH (1029_BGFD-N1-BDNA-1_2375WFLT3_s30) 8m 52s 1m 27s 6m 25s 1m 0s 5.3 GB 489% 232.0 GB 96.4 MB 0 bytes 76.0 MB 2
succeeded NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (1029_BGFD-N1-BDNA-1_2375WFLT3_s30) 8m 21s 1m 18s 6m 6s 57s 467.2 MB 776% 177.8 GB 83.4 MB 36.1 GB 79.3 MB 2
succeeded NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (1029_BGFD-N1-BDNA-1_2375WFLT3_s30;chr11_63291540-63291643) 7m 3s 3s 5m 51s 1m 9s 1.2 GB 228% 2.6 GB 1.2 MB 385.4 MB 1.2 MB 3
succeeded NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (1029_BGFD-N1-BDNA-1_2375WFLT3_s30;chr1_204140035-204140118) 7m 27s 1m 42s 4m 33s 1m 12s 1.7 GB 210% 2.6 GB 1.2 MB 2.4 GB 1.2 MB 1
succeeded NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (1029_BGFD-N1-BDNA-1_2375WFLT3_s30;chr12_122813270-122813419) 5m 16s 3s 4m 1s 1m 12s 1.2 GB 219% 2.3 GB 1.2 MB 460.7 MB 1.2 MB 3
succeeded NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (1029_BGFD-N1-BDNA-1_2375WFLT3_s30;chr15_81334720-81334975) 7m 3s 3s 5m 51s 1m 9s 1.4 GB 230% 2.7 GB 1.2 MB 280.0 MB 1.2 MB 3
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