Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_8GM-N1-BDNA-1_A23MHW3LT4_1/1029_8GM-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/f742131cd547e964a1ed6c84e81a6a/.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/ec/f742131cd547e964a1ed6c84e81a6a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_8GM-N1-BDNA-1_A23MHW3LT4_1/1029_8GM-N1-BDNA-1_A23MHW3LT4_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_8GM-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8GM-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8GM-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8GM-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: 99154354 total, 70945 skipped (flags/unmapped)
Fragments: 49791397 total (49244410 tlen-paired, 3234 hash-paired, 490 singletons, 19714 discordant, 523549 orphans, 12327 too large [>5000 bp], 15892724 duplicates)
Reads: 105514558 total, 58344 skipped (flags/unmapped)
Fragments: 52981271 total (52434208 tlen-paired, 3160 hash-paired, 596 singletons, 13923 discordant, 529384 orphans, 11826 too large [>5000 bp], 16686773 duplicates)
Reads: 114839369 total, 65891 skipped (flags/unmapped)
Fragments: 57668138 total (57037915 tlen-paired, 4029 hash-paired, 529 singletons, 19524 discordant, 606141 orphans, 21936 too large [>5000 bp], 18561216 duplicates)
Reads: 116131829 total, 104377 skipped (flags/unmapped)
Fragments: 58552891 total (56873628 tlen-paired, 4228 hash-paired, 554 singletons, 323569 discordant, 1350912 orphans, 136568 too large [>5000 bp], 18852661 duplicates)