Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_3g-N1-BDNA-1_B23MHTGLT4_1/659_3g-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/6daacade4ce92e4b15af875537f70a/.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/ea/6daacade4ce92e4b15af875537f70a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_3g-N1-BDNA-1_B23MHTGLT4_1/659_3g-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
==> 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: 659_3g-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_3g-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_3g-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_3g-N1-BDNA-1_B23MHTGLT4_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: 86252484 total, 65940 skipped (flags/unmapped)
Fragments: 43275653 total (42873862 tlen-paired, 4049 hash-paired, 379 singletons, 14974 discordant, 382389 orphans, 9003 too large [>5000 bp], 13455802 duplicates)
Reads: 91427881 total, 54234 skipped (flags/unmapped)
Fragments: 45871650 total (45469634 tlen-paired, 2836 hash-paired, 552 singletons, 9561 discordant, 389067 orphans, 9983 too large [>5000 bp], 14069365 duplicates)
Reads: 98689048 total, 60184 skipped (flags/unmapped)
Fragments: 49522793 total (49040684 tlen-paired, 7134 hash-paired, 377 singletons, 14995 discordant, 459603 orphans, 21629 too large [>5000 bp], 15564524 duplicates)
Reads: 100842003 total, 103734 skipped (flags/unmapped)
Fragments: 50761279 total (49536832 tlen-paired, 4550 hash-paired, 434 singletons, 236362 discordant, 983101 orphans, 99623 too large [>5000 bp], 15951191 duplicates)