Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/aih-tih-sc-32e1cf-N1_B23T7FYLT4_1/aih-tih-sc-32e1cf-N1_B23T7FYLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/aih-tih-sc-32e1cf-N1_B23T7FYLT4_1/aih-tih-sc-32e1cf-N1_B23T7FYLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/98fa26937b0f66a2fb1a5458b1be7f/.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/87/98fa26937b0f66a2fb1a5458b1be7f/.command.run
==> 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: aih-tih-sc-32e1cf-N1_B23T7FYLT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-32e1cf-N1_B23T7FYLT4_1.recalibrated.bam.bai

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-32e1cf-N1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-32e1cf-N1_B23T7FYLT4_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: 323251861 total, 243712 skipped (flags/unmapped)
Fragments: 162404290 total (160457540 tlen-paired, 16237 hash-paired, 1956 singletons, 47060 discordant, 1881497 orphans, 41511 too large [>5000 bp], 86109049 duplicates)
Reads: 349957147 total, 216395 skipped (flags/unmapped)
Fragments: 175851786 total (173693212 tlen-paired, 21657 hash-paired, 1785 singletons, 39305 discordant, 2095827 orphans, 67396 too large [>5000 bp], 94534399 duplicates)
Reads: 357558350 total, 213679 skipped (flags/unmapped)
Fragments: 179692290 total (177523729 tlen-paired, 19383 hash-paired, 2297 singletons, 33025 discordant, 2113856 orphans, 38122 too large [>5000 bp], 94870324 duplicates)
Reads: 392221900 total, 434932 skipped (flags/unmapped)
Fragments: 198039299 total (191211073 tlen-paired, 18326 hash-paired, 2451 singletons, 1406940 discordant, 5400509 orphans, 555665 too large [>5000 bp], 105692223 duplicates)