Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/d0cbf172260f6fd8165461788e4d16/.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/d0cbf172260f6fd8165461788e4d16/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_4Z5-N1-BDNA-1_B23KGCJLT4_1/1136_4Z5-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_4Z5-N1-BDNA-1_B23KGCJLT4_1/1136_4Z5-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
==> 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_4Z5-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4Z5-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4Z5-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4Z5-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: 47713630 total, 34008 skipped (flags/unmapped)
Fragments: 23907327 total (23750290 tlen-paired, 2020 hash-paired, 240 singletons, 7893 discordant, 146884 orphans, 6046 too large [>5000 bp], 8459555 duplicates)
Reads: 51310878 total, 30657 skipped (flags/unmapped)
Fragments: 25712964 total (25531025 tlen-paired, 2399 hash-paired, 227 singletons, 6985 discordant, 172328 orphans, 13424 too large [>5000 bp], 9103560 duplicates)
Reads: 51692850 total, 28206 skipped (flags/unmapped)
Fragments: 25901750 total (25743869 tlen-paired, 1956 hash-paired, 315 singletons, 5743 discordant, 149867 orphans, 5663 too large [>5000 bp], 8909358 duplicates)
Reads: 56596861 total, 46094 skipped (flags/unmapped)
Fragments: 28406851 total (27992234 tlen-paired, 1367 hash-paired, 192 singletons, 80287 discordant, 332771 orphans, 35014 too large [>5000 bp], 10070497 duplicates)