Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/4df917375fc07a82e7d10c9f37e40e/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_0YT-N1-BDNA-1_A23NMNVLT4_1/1136_0YT-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/4df917375fc07a82e7d10c9f37e40e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_0YT-N1-BDNA-1_A23NMNVLT4_1/1136_0YT-N1-BDNA-1_A23NMNVLT4_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_0YT-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YT-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YT-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0YT-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: 68273213 total, 55186 skipped (flags/unmapped)
Fragments: 34188650 total (34003484 tlen-paired, 2589 hash-paired, 293 singletons, 9364 discordant, 172920 orphans, 6970 too large [>5000 bp], 9504981 duplicates)
Reads: 74048929 total, 49643 skipped (flags/unmapped)
Fragments: 37086355 total (36873760 tlen-paired, 2424 hash-paired, 246 singletons, 8013 discordant, 201912 orphans, 14367 too large [>5000 bp], 10397687 duplicates)
Reads: 74349118 total, 46176 skipped (flags/unmapped)
Fragments: 37232441 total (37046076 tlen-paired, 2915 hash-paired, 305 singletons, 6430 discordant, 176715 orphans, 7540 too large [>5000 bp], 10131864 duplicates)
Reads: 81324350 total, 82005 skipped (flags/unmapped)
Fragments: 40779004 total (40283571 tlen-paired, 2755 hash-paired, 326 singletons, 95637 discordant, 396715 orphans, 40689 too large [>5000 bp], 11476995 duplicates)