Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/80745e0e6bcf53a5f74605419d3745/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_2BI-N1-BDNA-1_A23MHW3LT4_1/1136_2BI-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  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/66/80745e0e6bcf53a5f74605419d3745/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_2BI-N1-BDNA-1_A23MHW3LT4_1/1136_2BI-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] [W::hts_idx_load3] The index file is older than the data file: 1136_2BI-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_2BI-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_2BI-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2BI-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: 48558799 total, 32635 skipped (flags/unmapped)
Fragments: 24382519 total (24120602 tlen-paired, 1693 hash-paired, 282 singletons, 9414 discordant, 250528 orphans, 5968 too large [>5000 bp], 7426760 duplicates)
Reads: 51917138 total, 28642 skipped (flags/unmapped)
Fragments: 26065934 total (25800198 tlen-paired, 1746 hash-paired, 333 singletons, 6428 discordant, 257229 orphans, 7095 too large [>5000 bp], 7742268 duplicates)
Reads: 57149637 total, 49759 skipped (flags/unmapped)
Fragments: 28809561 total (27999938 tlen-paired, 1077 hash-paired, 247 singletons, 156840 discordant, 651459 orphans, 66231 too large [>5000 bp], 8771008 duplicates)
Reads: 56522754 total, 31727 skipped (flags/unmapped)
Fragments: 28381177 total (28076659 tlen-paired, 2004 hash-paired, 285 singletons, 9611 discordant, 292618 orphans, 10788 too large [>5000 bp], 8635271 duplicates)