Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BM04-N1-BDNA-1_A23KFG7LT4_1/1029_BM04-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/3062bd6cd1b3bb1381324cbb40bc9e/.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/c8/3062bd6cd1b3bb1381324cbb40bc9e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BM04-N1-BDNA-1_A23KFG7LT4_1/1029_BM04-N1-BDNA-1_A23KFG7LT4_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: 1029_BM04-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BM04-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BM04-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BM04-N1-BDNA-1_A23KFG7LT4_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: 71105232 total, 57199 skipped (flags/unmapped)
Fragments: 35861043 total (35154443 tlen-paired, 3800 hash-paired, 387 singletons, 8421 discordant, 693992 orphans, 10163 too large [>5000 bp], 15120344 duplicates)
Reads: 75281814 total, 49528 skipped (flags/unmapped)
Fragments: 37984424 total (37223828 tlen-paired, 2307 hash-paired, 503 singletons, 5795 discordant, 751991 orphans, 7966 too large [>5000 bp], 15546526 duplicates)
Reads: 82935325 total, 54362 skipped (flags/unmapped)
Fragments: 41844099 total (40977548 tlen-paired, 2956 hash-paired, 355 singletons, 8892 discordant, 854348 orphans, 23734 too large [>5000 bp], 17647287 duplicates)
Reads: 86182235 total, 95115 skipped (flags/unmapped)
Fragments: 43889930 total (41211841 tlen-paired, 4768 hash-paired, 522 singletons, 541067 discordant, 2131732 orphans, 219757 too large [>5000 bp], 18182303 duplicates)