Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/09ab65fd25bed39a2aa2c53d6c6c8b/.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/8a/09ab65fd25bed39a2aa2c53d6c6c8b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_F0L-N1-BDNA-1_B23KGCJLT4_1/1029_F0L-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_F0L-N1-BDNA-1_B23KGCJLT4_1/1029_F0L-N1-BDNA-1_B23KGCJLT4_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_F0L-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_F0L-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_F0L-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_F0L-N1-BDNA-1_B23KGCJLT4_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: 97272204 total, 59258 skipped (flags/unmapped)
Fragments: 48828090 total (48342122 tlen-paired, 3643 hash-paired, 604 singletons, 11199 discordant, 470522 orphans, 13946 too large [>5000 bp], 21488304 duplicates)
Reads: 91727292 total, 72864 skipped (flags/unmapped)
Fragments: 46031962 total (45567451 tlen-paired, 4741 hash-paired, 461 singletons, 15778 discordant, 443531 orphans, 17248 too large [>5000 bp], 20619107 duplicates)
Reads: 107951636 total, 64772 skipped (flags/unmapped)
Fragments: 54193121 total (53620734 tlen-paired, 7339 hash-paired, 386 singletons, 17082 discordant, 547580 orphans, 24294 too large [>5000 bp], 24327718 duplicates)
Reads: 109363722 total, 99476 skipped (flags/unmapped)
Fragments: 55106303 total (53625537 tlen-paired, 2937 hash-paired, 481 singletons, 290465 discordant, 1186883 orphans, 119502 too large [>5000 bp], 24615587 duplicates)