Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/2de6b65577deab4dfca41b8b7c5061/.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/a7/2de6b65577deab4dfca41b8b7c5061/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_10H-N1-BDNA-1_B23H2GYLT3_1/1136_10H-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1136_10H-N1-BDNA-1_B23H2GYLT3_1/1136_10H-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
==> 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_10H-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_10H-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_10H-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_10H-N1-BDNA-1_B23H2GYLT3_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: 77258145 total, 56500 skipped (flags/unmapped)
Fragments: 38799184 total (38350284 tlen-paired, 12463 hash-paired, 6001 singletons, 6926 discordant, 423510 orphans, 16394 too large [>5000 bp], 8431127 duplicates)
Reads: 76753345 total, 66840 skipped (flags/unmapped)
Fragments: 38533749 total (38117936 tlen-paired, 11555 hash-paired, 6236 singletons, 7109 discordant, 390913 orphans, 8078 too large [>5000 bp], 8427498 duplicates)
Reads: 84436275 total, 59434 skipped (flags/unmapped)
Fragments: 42407447 total (41933248 tlen-paired, 12193 hash-paired, 6714 singletons, 5491 discordant, 449801 orphans, 9231 too large [>5000 bp], 9229046 duplicates)
Reads: 86611864 total, 107232 skipped (flags/unmapped)
Fragments: 43714562 total (42271414 tlen-paired, 11791 hash-paired, 6877 singletons, 285207 discordant, 1139273 orphans, 110829 too large [>5000 bp], 9400101 duplicates)