Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/285ad907f74a4345724187bf09fd82/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/285ad907f74a4345724187bf09fd82/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1173_PCB-N1-BDNA-02_A23MHW3LT4_1/1173_PCB-N1-BDNA-02_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1173_PCB-N1-BDNA-02_A23MHW3LT4_1/1173_PCB-N1-BDNA-02_A23MHW3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1173_PCB-N1-BDNA-02_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_PCB-N1-BDNA-02_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_PCB-N1-BDNA-02_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_PCB-N1-BDNA-02_A23MHW3LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 89512353 total, 65272 skipped (flags/unmapped)
Fragments: 44969045 total (44430502 tlen-paired, 3837 hash-paired, 520 singletons, 18955 discordant, 515231 orphans, 12371 too large [>5000 bp], 15541548 duplicates)
Reads: 95104929 total, 54856 skipped (flags/unmapped)
Fragments: 47776143 total (47234825 tlen-paired, 3084 hash-paired, 642 singletons, 13183 discordant, 524409 orphans, 11419 too large [>5000 bp], 16267391 duplicates)
Reads: 104244274 total, 61790 skipped (flags/unmapped)
Fragments: 52368887 total (51740101 tlen-paired, 4299 hash-paired, 434 singletons, 19377 discordant, 604676 orphans, 24910 too large [>5000 bp], 18253537 duplicates)
Reads: 105976503 total, 95873 skipped (flags/unmapped)
Fragments: 53474909 total (51806940 tlen-paired, 3627 hash-paired, 521 singletons, 323958 discordant, 1339863 orphans, 135598 too large [>5000 bp], 18569839 duplicates)