Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/b992144eabf6cea5e91d73bbbf033b/.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/5a/b992144eabf6cea5e91d73bbbf033b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_1V8-N1-BDNA-1_A23H3W5LT3_1/1136_1V8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_1V8-N1-BDNA-1_A23H3W5LT3_1/1136_1V8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
==> 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: 1136_1V8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1V8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1V8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1V8-N1-BDNA-1_A23H3W5LT3_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: 73363634 total, 65181 skipped (flags/unmapped)
Fragments: 36828610 total (36437071 tlen-paired, 9725 hash-paired, 4746 singletons, 8693 discordant, 368375 orphans, 7177 too large [>5000 bp], 7835560 duplicates)
Reads: 79708135 total, 56756 skipped (flags/unmapped)
Fragments: 40023980 total (39593766 tlen-paired, 11137 hash-paired, 5024 singletons, 6306 discordant, 407747 orphans, 8095 too large [>5000 bp], 8512825 duplicates)
Reads: 82732903 total, 101040 skipped (flags/unmapped)
Fragments: 41744633 total (40418030 tlen-paired, 10383 hash-paired, 5214 singletons, 255941 discordant, 1055065 orphans, 101438 too large [>5000 bp], 8817423 duplicates)
Reads: 80931188 total, 60204 skipped (flags/unmapped)
Fragments: 40634868 total (40186456 tlen-paired, 13905 hash-paired, 4990 singletons, 8237 discordant, 421280 orphans, 13759 too large [>5000 bp], 8626631 duplicates)