Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_42D-N1-BDNA-1_A23H3NYLT3_1/1136_42D-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/02125d8a83ca33c11fd64bd4d1cda9/.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/f5/02125d8a83ca33c11fd64bd4d1cda9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_42D-N1-BDNA-1_A23H3NYLT3_1/1136_42D-N1-BDNA-1_A23H3NYLT3_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_42D-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_42D-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_42D-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_42D-N1-BDNA-1_A23H3NYLT3_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: 64982525 total, 56424 skipped (flags/unmapped)
Fragments: 32757087 total (32134642 tlen-paired, 7016 hash-paired, 6166 singletons, 6426 discordant, 602837 orphans, 10465 too large [>5000 bp], 4383405 duplicates)
Reads: 71884352 total, 56154 skipped (flags/unmapped)
Fragments: 36250597 total (35546767 tlen-paired, 6616 hash-paired, 6740 singletons, 6306 discordant, 684168 orphans, 8956 too large [>5000 bp], 4811077 duplicates)
Reads: 65631230 total, 64646 skipped (flags/unmapped)
Fragments: 33061622 total (32464718 tlen-paired, 6882 hash-paired, 6358 singletons, 7574 discordant, 576090 orphans, 12894 too large [>5000 bp], 4458160 duplicates)
Reads: 73189567 total, 90483 skipped (flags/unmapped)
Fragments: 37261462 total (35065120 tlen-paired, 5508 hash-paired, 6726 singletons, 444930 discordant, 1739178 orphans, 161032 too large [>5000 bp], 4861325 duplicates)