Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_dyR-N1-BDNA-1_A23TNVNLT4_1/659_dyR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/faa945baa10f1c6917b5e9d88394e1/.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/49/faa945baa10f1c6917b5e9d88394e1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_dyR-N1-BDNA-1_A23TNVNLT4_1/659_dyR-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: 659_dyR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_dyR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_dyR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_dyR-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: 84548473 total, 56945 skipped (flags/unmapped)
Fragments: 42414973 total (42038745 tlen-paired, 3658 hash-paired, 444 singletons, 12106 discordant, 360020 orphans, 11023 too large [>5000 bp], 14485738 duplicates)
Reads: 78067757 total, 68902 skipped (flags/unmapped)
Fragments: 39164526 total (38789599 tlen-paired, 5434 hash-paired, 425 singletons, 17964 discordant, 351104 orphans, 10666 too large [>5000 bp], 13482297 duplicates)
Reads: 93341966 total, 97973 skipped (flags/unmapped)
Fragments: 46967736 total (45905528 tlen-paired, 5071 hash-paired, 450 singletons, 204198 discordant, 852489 orphans, 80730 too large [>5000 bp], 16443013 duplicates)
Reads: 92229427 total, 60846 skipped (flags/unmapped)
Fragments: 46273638 total (45836113 tlen-paired, 6493 hash-paired, 422 singletons, 18821 discordant, 411789 orphans, 16758 too large [>5000 bp], 16268003 duplicates)