Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BI3C-N1-BDNA-1_B23H2GYLT3_1/1029_BI3C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/8bee87b1d58732bc52988ab537503e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BI3C-N1-BDNA-1_B23H2GYLT3_1/1029_BI3C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  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/38/8bee87b1d58732bc52988ab537503e/.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: 1029_BI3C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BI3C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BI3C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BI3C-N1-BDNA-1_B23H2GYLT3_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: 74820308 total, 63536 skipped (flags/unmapped)
Fragments: 37568849 total (37151269 tlen-paired, 12041 hash-paired, 6025 singletons, 7931 discordant, 391583 orphans, 8341 too large [>5000 bp], 7733534 duplicates)
Reads: 82117702 total, 54605 skipped (flags/unmapped)
Fragments: 41251124 total (40779261 tlen-paired, 11509 hash-paired, 6390 singletons, 5997 discordant, 447967 orphans, 7603 too large [>5000 bp], 8447341 duplicates)
Reads: 82642265 total, 58142 skipped (flags/unmapped)
Fragments: 41506911 total (41034852 tlen-paired, 12269 hash-paired, 6518 singletons, 8029 discordant, 445243 orphans, 11031 too large [>5000 bp], 8477165 duplicates)
Reads: 84779885 total, 96569 skipped (flags/unmapped)
Fragments: 42813954 total (41354118 tlen-paired, 11567 hash-paired, 6720 singletons, 284751 discordant, 1156798 orphans, 109463 too large [>5000 bp], 8652379 duplicates)