Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_CPH-N1-BDNA-1_A23H3NYLT3_1/869_CPH-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/8335bc4aa3eeacdd431db667c7c7f4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/8335bc4aa3eeacdd431db667c7c7f4/.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/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_CPH-N1-BDNA-1_A23H3NYLT3_1/869_CPH-N1-BDNA-1_A23H3NYLT3_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: 869_CPH-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_CPH-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 869_CPH-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 869_CPH-N1-BDNA-1_A23H3NYLT3_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: 87762940 total, 71418 skipped (flags/unmapped)
Fragments: 44003375 total (43630328 tlen-paired, 27733 hash-paired, 7968 singletons, 7232 discordant, 330114 orphans, 11427 too large [>5000 bp], 6081345 duplicates)
Reads: 94816519 total, 62587 skipped (flags/unmapped)
Fragments: 47559879 total (47138827 tlen-paired, 27701 hash-paired, 8617 singletons, 6117 discordant, 378617 orphans, 10704 too large [>5000 bp], 6534269 duplicates)
Reads: 95855321 total, 109832 skipped (flags/unmapped)
Fragments: 48259601 total (47052312 tlen-paired, 27908 hash-paired, 8627 singletons, 229300 discordant, 941454 orphans, 88184 too large [>5000 bp], 6579384 duplicates)
Reads: 94995830 total, 65112 skipped (flags/unmapped)
Fragments: 47641946 total (47217691 tlen-paired, 29677 hash-paired, 8854 singletons, 7646 discordant, 378078 orphans, 16879 too large [>5000 bp], 6539894 duplicates)