Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/0a91f474e233f1788df791343d33e8/.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/bf/0a91f474e233f1788df791343d33e8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BAPK-N1-BDNA-1_A23TNVNLT4_1/1241_BAPK-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BAPK-N1-BDNA-1_A23TNVNLT4_1/1241_BAPK-N1-BDNA-1_A23TNVNLT4_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: 1241_BAPK-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BAPK-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BAPK-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BAPK-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: 82847329 total, 58579 skipped (flags/unmapped)
Fragments: 41547076 total (41203190 tlen-paired, 4306 hash-paired, 354 singletons, 14478 discordant, 324748 orphans, 9850 too large [>5000 bp], 15841578 duplicates)
Reads: 88956213 total, 50071 skipped (flags/unmapped)
Fragments: 44615594 total (44257140 tlen-paired, 3272 hash-paired, 430 singletons, 10212 discordant, 344540 orphans, 9962 too large [>5000 bp], 16625608 duplicates)
Reads: 88702308 total, 50735 skipped (flags/unmapped)
Fragments: 44490695 total (44114042 tlen-paired, 3554 hash-paired, 338 singletons, 12314 discordant, 360447 orphans, 15484 too large [>5000 bp], 17038565 duplicates)
Reads: 97696509 total, 92655 skipped (flags/unmapped)
Fragments: 49124882 total (48112075 tlen-paired, 3992 hash-paired, 426 singletons, 200167 discordant, 808222 orphans, 81369 too large [>5000 bp], 18795768 duplicates)