Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_CH-N1-BDNA-1_A23TNVNLT4_1/1267_CH-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_CH-N1-BDNA-1_A23TNVNLT4_1/1267_CH-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/7edc57238e2733c6ff0672e1b5b40e/.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/d3/7edc57238e2733c6ff0672e1b5b40e/.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: 1267_CH-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_CH-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_CH-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_CH-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: 60351030 total, 43498 skipped (flags/unmapped)
Fragments: 30278795 total (30001407 tlen-paired, 3195 hash-paired, 260 singletons, 11583 discordant, 262350 orphans, 6276 too large [>5000 bp], 10810758 duplicates)
Reads: 64903623 total, 35820 skipped (flags/unmapped)
Fragments: 32567953 total (32277102 tlen-paired, 2183 hash-paired, 339 singletons, 8111 discordant, 280218 orphans, 6227 too large [>5000 bp], 11370343 duplicates)
Reads: 71043128 total, 38170 skipped (flags/unmapped)
Fragments: 35647427 total (35318952 tlen-paired, 2522 hash-paired, 284 singletons, 11313 discordant, 314356 orphans, 12372 too large [>5000 bp], 12765061 duplicates)
Reads: 72301947 total, 67780 skipped (flags/unmapped)
Fragments: 36392974 total (35541477 tlen-paired, 3298 hash-paired, 292 singletons, 166232 discordant, 681675 orphans, 65093 too large [>5000 bp], 13003233 duplicates)