Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/2744b91ed62d3d81dde7a7cb9eca34/.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/86/2744b91ed62d3d81dde7a7cb9eca34/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_S6U-N1-BDNA-1_B23H3Y2LT3_1/869_S6U-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_S6U-N1-BDNA-1_B23H3Y2LT3_1/869_S6U-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_S6U-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.baiThe index file is older than the data file: 869_S6U-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_S6U-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_S6U-N1-BDNA-1_B23H3Y2LT3_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: 69795340 total, 77855 skipped (flags/unmapped)
Fragments: 35121972 total (34560978 tlen-paired, 7904 hash-paired, 2438 singletons, 7117 discordant, 543535 orphans, 9757 too large [>5000 bp], 6803253 duplicates)
Reads: 75669171 total, 64233 skipped (flags/unmapped)
Fragments: 38101640 total (37476138 tlen-paired, 7676 hash-paired, 2615 singletons, 4860 discordant, 610351 orphans, 7312 too large [>5000 bp], 7352403 duplicates)
Reads: 76588090 total, 65678 skipped (flags/unmapped)
Fragments: 38559359 total (37914980 tlen-paired, 8660 hash-paired, 2531 singletons, 7551 discordant, 625637 orphans, 15931 too large [>5000 bp], 7414283 duplicates)
Reads: 79204582 total, 166980 skipped (flags/unmapped)
Fragments: 40189357 total (38114544 tlen-paired, 8367 hash-paired, 2875 singletons, 406212 discordant, 1657359 orphans, 159561 too large [>5000 bp], 7585406 duplicates)