Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_0-N1-BDNA-1_A23TNVNLT4_1/1267_0-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/cbab52046e78f2c09773a59538aa65/.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/76/cbab52046e78f2c09773a59538aa65/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_0-N1-BDNA-1_A23TNVNLT4_1/1267_0-N1-BDNA-1_A23TNVNLT4_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: 1267_0-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_0-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_0-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_0-N1-BDNA-1_A23TNVNLT4_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: 69470322 total, 48971 skipped (flags/unmapped)
Fragments: 34811604 total (34580073 tlen-paired, 2849 hash-paired, 343 singletons, 11645 discordant, 216694 orphans, 7590 too large [>5000 bp], 12194299 duplicates)
Reads: 74412826 total, 42683 skipped (flags/unmapped)
Fragments: 37289071 total (37055247 tlen-paired, 2129 hash-paired, 376 singletons, 8244 discordant, 223075 orphans, 7726 too large [>5000 bp], 12830070 duplicates)
Reads: 82071673 total, 81811 skipped (flags/unmapped)
Fragments: 41201799 total (40568291 tlen-paired, 2846 hash-paired, 349 singletons, 119760 discordant, 510553 orphans, 48583 too large [>5000 bp], 14531004 duplicates)
Reads: 81456782 total, 45694 skipped (flags/unmapped)
Fragments: 40821375 total (40551583 tlen-paired, 3127 hash-paired, 307 singletons, 12077 discordant, 254281 orphans, 11463 too large [>5000 bp], 14379917 duplicates)