Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/2d9e9ad06e7084b68fe434cb963d2b/.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/c7/2d9e9ad06e7084b68fe434cb963d2b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_W80-N1-BDNA-1_A23MHW3LT4_1/1029_W80-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_W80-N1-BDNA-1_A23MHW3LT4_1/1029_W80-N1-BDNA-1_A23MHW3LT4_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: 1029_W80-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_W80-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_W80-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_W80-N1-BDNA-1_A23MHW3LT4_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: 94633337 total, 53982 skipped (flags/unmapped)
Fragments: 47529020 total (47016550 tlen-paired, 2455 hash-paired, 609 singletons, 11366 discordant, 498040 orphans, 9982 too large [>5000 bp], 16460128 duplicates)
Reads: 89376011 total, 64331 skipped (flags/unmapped)
Fragments: 44886229 total (44378274 tlen-paired, 3626 hash-paired, 504 singletons, 17071 discordant, 486754 orphans, 13240 too large [>5000 bp], 15846777 duplicates)
Reads: 104042681 total, 96494 skipped (flags/unmapped)
Fragments: 52487662 total (50891926 tlen-paired, 2735 hash-paired, 561 singletons, 309034 discordant, 1283406 orphans, 127415 too large [>5000 bp], 18575492 duplicates)
Reads: 102867394 total, 61240 skipped (flags/unmapped)
Fragments: 51666007 total (51087028 tlen-paired, 4518 hash-paired, 492 singletons, 17079 discordant, 556890 orphans, 15761 too large [>5000 bp], 18325769 duplicates)