Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_75V-N1-BDNA-1_A23H3NYLT3_1/1136_75V-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_75V-N1-BDNA-1_A23H3NYLT3_1/1136_75V-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/e63f7e98e65682665f0ff372c8b53e/.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/ed/e63f7e98e65682665f0ff372c8b53e/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_75V-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_75V-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_75V-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_75V-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: 73921714 total, 70261 skipped (flags/unmapped)
Fragments: 37223008 total (36587288 tlen-paired, 10324 hash-paired, 6933 singletons, 9935 discordant, 608528 orphans, 10449 too large [>5000 bp], 5943787 duplicates)
Reads: 73263896 total, 59125 skipped (flags/unmapped)
Fragments: 36909222 total (36259495 tlen-paired, 10306 hash-paired, 6807 singletons, 8056 discordant, 624558 orphans, 8846 too large [>5000 bp], 5887006 duplicates)
Reads: 80256983 total, 59281 skipped (flags/unmapped)
Fragments: 40444051 total (39715574 tlen-paired, 10264 hash-paired, 7329 singletons, 7811 discordant, 703073 orphans, 10001 too large [>5000 bp], 6374510 duplicates)
Reads: 82208274 total, 107664 skipped (flags/unmapped)
Fragments: 41780795 total (39512197 tlen-paired, 10323 hash-paired, 7719 singletons, 455699 discordant, 1794857 orphans, 170798 too large [>5000 bp], 6516820 duplicates)