Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/0f3128054003f7e6d0265eee18ac13/.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/40/0f3128054003f7e6d0265eee18ac13/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_2GM-N1-BDNA-1_A23MHW3LT4_1/1136_2GM-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_2GM-N1-BDNA-1_A23MHW3LT4_1/1136_2GM-N1-BDNA-1_A23MHW3LT4_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: 1136_2GM-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_2GM-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2GM-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2GM-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: 88972559 total, 65595 skipped (flags/unmapped)
Fragments: 44679452 total (44185533 tlen-paired, 2938 hash-paired, 446 singletons, 16311 discordant, 474224 orphans, 11365 too large [>5000 bp], 15859787 duplicates)
Reads: 95031898 total, 58323 skipped (flags/unmapped)
Fragments: 47717449 total (47212433 tlen-paired, 3479 hash-paired, 659 singletons, 11190 discordant, 489688 orphans, 14512 too large [>5000 bp], 16599837 duplicates)
Reads: 103909072 total, 63418 skipped (flags/unmapped)
Fragments: 52184205 total (51604580 tlen-paired, 5252 hash-paired, 544 singletons, 16509 discordant, 557320 orphans, 17554 too large [>5000 bp], 18570315 duplicates)
Reads: 105054771 total, 106207 skipped (flags/unmapped)
Fragments: 52975593 total (51410235 tlen-paired, 3715 hash-paired, 562 singletons, 304123 discordant, 1256958 orphans, 127449 too large [>5000 bp], 18804029 duplicates)