Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/0484664df151fbd6f6ef06a2b46df7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_4EF-N1-BDNA-1_B23KGCJLT4_1/1136_4EF-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  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/a4/0484664df151fbd6f6ef06a2b46df7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_4EF-N1-BDNA-1_B23KGCJLT4_1/1136_4EF-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> 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_4EF-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4EF-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4EF-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4EF-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: 73149298 total, 50587 skipped (flags/unmapped)
Fragments: 36647644 total (36416065 tlen-paired, 3365 hash-paired, 383 singletons, 12569 discordant, 215262 orphans, 9534 too large [>5000 bp], 14512244 duplicates)
Reads: 77784864 total, 46226 skipped (flags/unmapped)
Fragments: 38968328 total (38739483 tlen-paired, 2781 hash-paired, 328 singletons, 8326 discordant, 217410 orphans, 9860 too large [>5000 bp], 15125223 duplicates)
Reads: 86149575 total, 49460 skipped (flags/unmapped)
Fragments: 43164357 total (42874711 tlen-paired, 4859 hash-paired, 309 singletons, 12140 discordant, 272338 orphans, 22024 too large [>5000 bp], 17147474 duplicates)
Reads: 86543945 total, 74076 skipped (flags/unmapped)
Fragments: 43432785 total (42821923 tlen-paired, 2655 hash-paired, 350 singletons, 115068 discordant, 492789 orphans, 48719 too large [>5000 bp], 17292109 duplicates)