Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/88b8ca9cfedb427ad446d87e81f872/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_024-N1-BDNA-1_B23H2GYLT3_1/1136_024-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  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/02/88b8ca9cfedb427ad446d87e81f872/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_024-N1-BDNA-1_B23H2GYLT3_1/1136_024-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_024-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_024-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_024-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_024-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: 97179045 total, 90183 skipped (flags/unmapped)
Fragments: 48810488 total (48233470 tlen-paired, 13696 hash-paired, 8042 singletons, 10786 discordant, 544494 orphans, 10211 too large [>5000 bp], 12468624 duplicates)
Reads: 107307771 total, 84154 skipped (flags/unmapped)
Fragments: 53913722 total (53243693 tlen-paired, 14181 hash-paired, 8746 singletons, 10825 discordant, 636277 orphans, 20598 too large [>5000 bp], 13680995 duplicates)
Reads: 105871924 total, 82521 skipped (flags/unmapped)
Fragments: 53202805 total (52540282 tlen-paired, 14206 hash-paired, 8572 singletons, 7630 discordant, 632115 orphans, 12240 too large [>5000 bp], 13573298 duplicates)
Reads: 110420750 total, 145356 skipped (flags/unmapped)
Fragments: 55806770 total (53741798 tlen-paired, 13934 hash-paired, 9206 singletons, 406284 discordant, 1635548 orphans, 153304 too large [>5000 bp], 13978923 duplicates)