Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/cba6901d9f33e9beb97fa2f8fa7cc2/.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/50/cba6901d9f33e9beb97fa2f8fa7cc2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1029_XI2-N1-BDNA-1_A23H3NYLT3_1/1029_XI2-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1029_XI2-N1-BDNA-1_A23H3NYLT3_1/1029_XI2-N1-BDNA-1_A23H3NYLT3_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: 1029_XI2-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_XI2-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_XI2-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_XI2-N1-BDNA-1_A23H3NYLT3_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: 73214087 total, 71124 skipped (flags/unmapped)
Fragments: 36764909 total (36331765 tlen-paired, 15740 hash-paired, 8033 singletons, 8081 discordant, 401290 orphans, 11234 too large [>5000 bp], 5950728 duplicates)
Reads: 78977935 total, 65335 skipped (flags/unmapped)
Fragments: 39673603 total (39188073 tlen-paired, 15685 hash-paired, 8692 singletons, 8445 discordant, 452708 orphans, 13397 too large [>5000 bp], 6382295 duplicates)
Reads: 80555015 total, 105563 skipped (flags/unmapped)
Fragments: 40709364 total (39220382 tlen-paired, 14972 hash-paired, 8581 singletons, 288342 discordant, 1177087 orphans, 108196 too large [>5000 bp], 6470291 duplicates)
Reads: 79304505 total, 61475 skipped (flags/unmapped)
Fragments: 39848389 total (39351466 tlen-paired, 16783 hash-paired, 8599 singletons, 6700 discordant, 464841 orphans, 9846 too large [>5000 bp], 6362687 duplicates)