Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_3Y2-N1-BDNA-1_A23NMNVLT4_1/1136_3Y2-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_3Y2-N1-BDNA-1_A23NMNVLT4_1/1136_3Y2-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/084935a3d089d4572a8734926a7723/.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/11/084935a3d089d4572a8734926a7723/.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: 1136_3Y2-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_3Y2-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3Y2-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3Y2-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: 69701018 total, 53811 skipped (flags/unmapped)
Fragments: 34916893 total (34698280 tlen-paired, 2649 hash-paired, 351 singletons, 11683 discordant, 203930 orphans, 8851 too large [>5000 bp], 10233949 duplicates)
Reads: 75227713 total, 45433 skipped (flags/unmapped)
Fragments: 37687643 total (37468255 tlen-paired, 2757 hash-paired, 334 singletons, 8073 discordant, 208224 orphans, 7776 too large [>5000 bp], 10878397 duplicates)
Reads: 75451148 total, 47890 skipped (flags/unmapped)
Fragments: 37804621 total (37558597 tlen-paired, 3195 hash-paired, 286 singletons, 10333 discordant, 232210 orphans, 13256 too large [>5000 bp], 11203860 duplicates)
Reads: 82904284 total, 77370 skipped (flags/unmapped)
Fragments: 41598934 total (41023252 tlen-paired, 2261 hash-paired, 332 singletons, 110921 discordant, 462168 orphans, 45773 too large [>5000 bp], 12358799 duplicates)