Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_031-N1-BDNA-1_A23NMNVLT4_1/1136_031-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/0758d770a33afbbed998c4667215b4/.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/20/0758d770a33afbbed998c4667215b4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_031-N1-BDNA-1_A23NMNVLT4_1/1136_031-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] [W::hts_idx_load3] The index file is older than the data file: 1136_031-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_031-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_031-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_031-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: 94504250 total, 54116 skipped (flags/unmapped)
Fragments: 47313022 total (47109523 tlen-paired, 3207 hash-paired, 363 singletons, 7536 discordant, 192393 orphans, 8423 too large [>5000 bp], 14115561 duplicates)
Reads: 86897256 total, 66058 skipped (flags/unmapped)
Fragments: 43500549 total (43298313 tlen-paired, 2974 hash-paired, 320 singletons, 10578 discordant, 188364 orphans, 9392 too large [>5000 bp], 13169017 duplicates)
Reads: 93824568 total, 57825 skipped (flags/unmapped)
Fragments: 46979347 total (46729014 tlen-paired, 4370 hash-paired, 283 singletons, 9704 discordant, 235976 orphans, 22154 too large [>5000 bp], 14333818 duplicates)
Reads: 103603301 total, 93843 skipped (flags/unmapped)
Fragments: 51924124 total (51396237 tlen-paired, 3229 hash-paired, 368 singletons, 101182 discordant, 423108 orphans, 42343 too large [>5000 bp], 15890848 duplicates)