Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_8DV-N1-BDNA-1_B23KGCJLT4_1/1136_8DV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/79624bc3888f6a593b3e562f265429/.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/4e/79624bc3888f6a593b3e562f265429/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_8DV-N1-BDNA-1_B23KGCJLT4_1/1136_8DV-N1-BDNA-1_B23KGCJLT4_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_8DV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DV-N1-BDNA-1_B23KGCJLT4_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: 74466236 total, 53721 skipped (flags/unmapped)
Fragments: 37313750 total (37064329 tlen-paired, 2811 hash-paired, 344 singletons, 10919 discordant, 235347 orphans, 10353 too large [>5000 bp], 14261962 duplicates)
Reads: 79800079 total, 49201 skipped (flags/unmapped)
Fragments: 39985275 total (39730789 tlen-paired, 4170 hash-paired, 351 singletons, 7424 discordant, 242541 orphans, 11610 too large [>5000 bp], 14981082 duplicates)
Reads: 87867989 total, 51971 skipped (flags/unmapped)
Fragments: 44034838 total (43727939 tlen-paired, 5016 hash-paired, 338 singletons, 11079 discordant, 290466 orphans, 18573 too large [>5000 bp], 16917639 duplicates)
Reads: 88124831 total, 74382 skipped (flags/unmapped)
Fragments: 44255924 total (43537225 tlen-paired, 1874 hash-paired, 326 singletons, 138414 discordant, 578085 orphans, 58506 too large [>5000 bp], 17023948 duplicates)