Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1047_FF-N1-BDNA-1_A23NMNVLT4_1/1047_FF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/d4e3786d0eb13e43425d0217d65d49/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1047_FF-N1-BDNA-1_A23NMNVLT4_1/1047_FF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  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/8d/d4e3786d0eb13e43425d0217d65d49/.command.run
==> 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: 1047_FF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_FF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_FF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_FF-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: 66882805 total, 42526 skipped (flags/unmapped)
Fragments: 33512087 total (33286904 tlen-paired, 3182 hash-paired, 265 singletons, 8018 discordant, 213718 orphans, 15044 too large [>5000 bp], 9527592 duplicates)
Reads: 61830342 total, 46714 skipped (flags/unmapped)
Fragments: 30975701 total (30783488 tlen-paired, 2514 hash-paired, 276 singletons, 8593 discordant, 180830 orphans, 6666 too large [>5000 bp], 8718279 duplicates)
Reads: 66869203 total, 37804 skipped (flags/unmapped)
Fragments: 33502343 total (33306502 tlen-paired, 2421 hash-paired, 255 singletons, 5865 discordant, 187300 orphans, 7134 too large [>5000 bp], 9277893 duplicates)
Reads: 73721035 total, 68585 skipped (flags/unmapped)
Fragments: 37000259 total (36450570 tlen-paired, 2442 hash-paired, 277 singletons, 107775 discordant, 439195 orphans, 45702 too large [>5000 bp], 10549600 duplicates)