Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_KAT-N1-BDNA-1_B23H3Y2LT3_1/869_KAT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/9ac387b17edfd95d5690d934d5e29e/.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/cf/9ac387b17edfd95d5690d934d5e29e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_KAT-N1-BDNA-1_B23H3Y2LT3_1/869_KAT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
==> 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: 869_KAT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
The index file is older than the data file: 869_KAT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_KAT-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_KAT-N1-BDNA-1_B23H3Y2LT3_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: 73028810 total, 74723 skipped (flags/unmapped)
Fragments: 36750252 total (36171316 tlen-paired, 8572 hash-paired, 2526 singletons, 8457 discordant, 559381 orphans, 7745 too large [>5000 bp], 8134484 duplicates)
Reads: 73639134 total, 62972 skipped (flags/unmapped)
Fragments: 37074736 total (36454937 tlen-paired, 8842 hash-paired, 2435 singletons, 7637 discordant, 600885 orphans, 15005 too large [>5000 bp], 8166142 duplicates)
Reads: 79981970 total, 63805 skipped (flags/unmapped)
Fragments: 40270886 total (39615499 tlen-paired, 9357 hash-paired, 2797 singletons, 5917 discordant, 637316 orphans, 8253 too large [>5000 bp], 8873432 duplicates)
Reads: 83327681 total, 161001 skipped (flags/unmapped)
Fragments: 42252265 total (40156061 tlen-paired, 10861 hash-paired, 2827 singletons, 421373 discordant, 1661143 orphans, 163060 too large [>5000 bp], 9191780 duplicates)