Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BNM7-N1-BDNA-1_B23H2GYLT3_1/1029_BNM7-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/ce00bfe8b097d731651cc9686967d3/.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/12/ce00bfe8b097d731651cc9686967d3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BNM7-N1-BDNA-1_B23H2GYLT3_1/1029_BNM7-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_BNM7-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNM7-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNM7-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNM7-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: 68244773 total, 62422 skipped (flags/unmapped)
Fragments: 34327067 total (33826624 tlen-paired, 6371 hash-paired, 5532 singletons, 7185 discordant, 481355 orphans, 7552 too large [>5000 bp], 6712965 duplicates)
Reads: 75218844 total, 57156 skipped (flags/unmapped)
Fragments: 37852583 total (37265315 tlen-paired, 7731 hash-paired, 5783 singletons, 7257 discordant, 566497 orphans, 14401 too large [>5000 bp], 7357354 duplicates)
Reads: 76105380 total, 53584 skipped (flags/unmapped)
Fragments: 38308909 total (37714598 tlen-paired, 6203 hash-paired, 5929 singletons, 5362 discordant, 576817 orphans, 8362 too large [>5000 bp], 7492479 duplicates)
Reads: 77405158 total, 97361 skipped (flags/unmapped)
Fragments: 39268153 total (37389762 tlen-paired, 7223 hash-paired, 6110 singletons, 367051 discordant, 1498007 orphans, 137804 too large [>5000 bp], 7525672 duplicates)