Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_0B1-N1-BDNA-1_B23KGCJLT4_1/1136_0B1-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/9ec129ca07fc34603c4167ead1972a/.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/6c/9ec129ca07fc34603c4167ead1972a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_0B1-N1-BDNA-1_B23KGCJLT4_1/1136_0B1-N1-BDNA-1_B23KGCJLT4_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: 1136_0B1-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0B1-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0B1-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0B1-N1-BDNA-1_B23KGCJLT4_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: 78099051 total, 43970 skipped (flags/unmapped)
Fragments: 39145569 total (38878617 tlen-paired, 2145 hash-paired, 447 singletons, 10204 discordant, 254156 orphans, 9273 too large [>5000 bp], 15126252 duplicates)
Reads: 73161319 total, 53535 skipped (flags/unmapped)
Fragments: 36667745 total (36397601 tlen-paired, 2912 hash-paired, 369 singletons, 14662 discordant, 252201 orphans, 12432 too large [>5000 bp], 14442389 duplicates)
Reads: 85708788 total, 48518 skipped (flags/unmapped)
Fragments: 42962201 total (42627212 tlen-paired, 5580 hash-paired, 317 singletons, 15137 discordant, 313955 orphans, 25070 too large [>5000 bp], 16998673 duplicates)
Reads: 86284932 total, 77079 skipped (flags/unmapped)
Fragments: 43330711 total (42631759 tlen-paired, 2444 hash-paired, 400 singletons, 130865 discordant, 565243 orphans, 56037 too large [>5000 bp], 17135300 duplicates)