Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BD0T-N1-BDNA-1_A23TNVNLT4_1/1241_BD0T-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/3119cb752fd0690af7339805f67009/.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/8a/3119cb752fd0690af7339805f67009/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BD0T-N1-BDNA-1_A23TNVNLT4_1/1241_BD0T-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_BD0T-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BD0T-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BD0T-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BD0T-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: 80451938 total, 56432 skipped (flags/unmapped)
Fragments: 40310841 total (40050748 tlen-paired, 3292 hash-paired, 350 singletons, 13641 discordant, 242810 orphans, 8492 too large [>5000 bp], 13990472 duplicates)
Reads: 88262691 total, 49461 skipped (flags/unmapped)
Fragments: 44224580 total (43957171 tlen-paired, 3424 hash-paired, 421 singletons, 9719 discordant, 253845 orphans, 9168 too large [>5000 bp], 15070133 duplicates)
Reads: 95284878 total, 96625 skipped (flags/unmapped)
Fragments: 47823170 total (47122843 tlen-paired, 3495 hash-paired, 409 singletons, 131397 discordant, 565026 orphans, 53674 too large [>5000 bp], 16674335 duplicates)
Reads: 94296845 total, 54801 skipped (flags/unmapped)
Fragments: 47247793 total (46940144 tlen-paired, 5976 hash-paired, 377 singletons, 14409 discordant, 286887 orphans, 16861 too large [>5000 bp], 16462336 duplicates)