Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/02212ba520d852e1a26212e4aa80a6/.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/38/02212ba520d852e1a26212e4aa80a6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_C3S-N1-BDNA-1_B23H2GYLT3_1/1029_C3S-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_C3S-N1-BDNA-1_B23H2GYLT3_1/1029_C3S-N1-BDNA-1_B23H2GYLT3_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_C3S-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_C3S-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_C3S-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_C3S-N1-BDNA-1_B23H2GYLT3_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: 83301243 total, 72141 skipped (flags/unmapped)
Fragments: 41849736 total (41348454 tlen-paired, 8543 hash-paired, 6471 singletons, 7011 discordant, 479257 orphans, 7679 too large [>5000 bp], 8869117 duplicates)
Reads: 91873265 total, 64512 skipped (flags/unmapped)
Fragments: 46174196 total (45595024 tlen-paired, 8915 hash-paired, 6762 singletons, 7170 discordant, 556325 orphans, 11724 too large [>5000 bp], 9685726 duplicates)
Reads: 91162944 total, 63307 skipped (flags/unmapped)
Fragments: 45828961 total (45236519 tlen-paired, 8701 hash-paired, 6512 singletons, 4984 discordant, 572245 orphans, 10236 too large [>5000 bp], 9629613 duplicates)
Reads: 94737507 total, 108798 skipped (flags/unmapped)
Fragments: 47925050 total (46046252 tlen-paired, 9574 hash-paired, 6890 singletons, 373725 discordant, 1488609 orphans, 137054 too large [>5000 bp], 9917376 duplicates)