Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_cvg-N1-BDNA-1_A23TNVNLT4_1/659_cvg-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/659_cvg-N1-BDNA-1_A23TNVNLT4_1/659_cvg-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/3e4dc28b0d2ee4ca4fb3a39cc93248/.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/36/3e4dc28b0d2ee4ca4fb3a39cc93248/.command.run
==> 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: 659_cvg-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cvg-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cvg-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cvg-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: 77678093 total, 51403 skipped (flags/unmapped)
Fragments: 38956287 total (38640256 tlen-paired, 3136 hash-paired, 342 singletons, 11935 discordant, 300618 orphans, 7538 too large [>5000 bp], 13582592 duplicates)
Reads: 84522161 total, 44533 skipped (flags/unmapped)
Fragments: 42392287 total (42056781 tlen-paired, 2810 hash-paired, 439 singletons, 8766 discordant, 323491 orphans, 8492 too large [>5000 bp], 14465837 duplicates)
Reads: 83196360 total, 47432 skipped (flags/unmapped)
Fragments: 41727296 total (41369087 tlen-paired, 5219 hash-paired, 316 singletons, 10592 discordant, 342082 orphans, 18367 too large [>5000 bp], 14636459 duplicates)
Reads: 92364187 total, 88821 skipped (flags/unmapped)
Fragments: 46447736 total (45474286 tlen-paired, 3360 hash-paired, 502 singletons, 194336 discordant, 775252 orphans, 77824 too large [>5000 bp], 16271261 duplicates)