Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_Q3Y-N1-BDNA-1_A23MHW3LT4_1/1029_Q3Y-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/46d21d71e72aca5304af5e34cee10e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/46d21d71e72aca5304af5e34cee10e/.command.run
  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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_Q3Y-N1-BDNA-1_A23MHW3LT4_1/1029_Q3Y-N1-BDNA-1_A23MHW3LT4_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: 1029_Q3Y-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_Q3Y-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_Q3Y-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_Q3Y-N1-BDNA-1_A23MHW3LT4_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: 72625990 total, 59435 skipped (flags/unmapped)
Fragments: 36550101 total (35979534 tlen-paired, 3037 hash-paired, 469 singletons, 15439 discordant, 551622 orphans, 9222 too large [>5000 bp], 13018201 duplicates)
Reads: 76783576 total, 52001 skipped (flags/unmapped)
Fragments: 38639005 total (38058931 tlen-paired, 2453 hash-paired, 498 singletons, 10106 discordant, 567017 orphans, 10540 too large [>5000 bp], 13465651 duplicates)
Reads: 84186450 total, 59013 skipped (flags/unmapped)
Fragments: 42367811 total (41688204 tlen-paired, 4698 hash-paired, 428 singletons, 14398 discordant, 660083 orphans, 26163 too large [>5000 bp], 15088437 duplicates)
Reads: 85376522 total, 96120 skipped (flags/unmapped)
Fragments: 43250134 total (41337926 tlen-paired, 3198 hash-paired, 478 singletons, 373980 discordant, 1534552 orphans, 157582 too large [>5000 bp], 15283793 duplicates)