Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_bOn-N1-BDNA-1_A23TNVNLT4_1/659_bOn-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_bOn-N1-BDNA-1_A23TNVNLT4_1/659_bOn-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/0db7522db935fc6cb9db1bc3d92bfb/.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/2a/0db7522db935fc6cb9db1bc3d92bfb/.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: 659_bOn-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bOn-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bOn-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bOn-N1-BDNA-1_A23TNVNLT4_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: 70717305 total, 46663 skipped (flags/unmapped)
Fragments: 35451269 total (35186538 tlen-paired, 2989 hash-paired, 267 singletons, 10938 discordant, 250537 orphans, 9454 too large [>5000 bp], 12055649 duplicates)
Reads: 76019933 total, 39951 skipped (flags/unmapped)
Fragments: 38115440 total (37823783 tlen-paired, 2398 hash-paired, 232 singletons, 9079 discordant, 279948 orphans, 14641 too large [>5000 bp], 13124122 duplicates)
Reads: 76107612 total, 40273 skipped (flags/unmapped)
Fragments: 38157917 total (37883870 tlen-paired, 2482 hash-paired, 306 singletons, 7508 discordant, 263751 orphans, 7781 too large [>5000 bp], 12719914 duplicates)
Reads: 84333731 total, 74204 skipped (flags/unmapped)
Fragments: 42381001 total (41589777 tlen-paired, 2702 hash-paired, 301 singletons, 159015 discordant, 629206 orphans, 63516 too large [>5000 bp], 14598814 duplicates)