Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_6L3-N1-BDNA-1_A23NMNVLT4_1/1136_6L3-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/e80f015fb89d436da735914f7809e1/.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/79/e80f015fb89d436da735914f7809e1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_6L3-N1-BDNA-1_A23NMNVLT4_1/1136_6L3-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6L3-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6L3-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6L3-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6L3-N1-BDNA-1_A23NMNVLT4_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: 59942182 total, 47595 skipped (flags/unmapped)
Fragments: 30025861 total (29842721 tlen-paired, 2200 hash-paired, 253 singletons, 9537 discordant, 171150 orphans, 7134 too large [>5000 bp], 8015333 duplicates)
Reads: 64478790 total, 39066 skipped (flags/unmapped)
Fragments: 32301039 total (32116277 tlen-paired, 2031 hash-paired, 241 singletons, 6097 discordant, 176393 orphans, 7140 too large [>5000 bp], 8506239 duplicates)
Reads: 71321060 total, 71273 skipped (flags/unmapped)
Fragments: 35787490 total (35286997 tlen-paired, 2358 hash-paired, 303 singletons, 94106 discordant, 403726 orphans, 39418 too large [>5000 bp], 9663063 duplicates)
Reads: 70960693 total, 44067 skipped (flags/unmapped)
Fragments: 35551158 total (35324097 tlen-paired, 2877 hash-paired, 234 singletons, 9566 discordant, 214384 orphans, 14464 too large [>5000 bp], 9582058 duplicates)