Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/cfb5487a8821291e79dc2e4c20177a/.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/1f/cfb5487a8821291e79dc2e4c20177a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_64O-N1-BDNA-1_A23MHW3LT4_1/1029_64O-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_64O-N1-BDNA-1_A23MHW3LT4_1/1029_64O-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_64O-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_64O-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_64O-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_64O-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: 62967656 total, 44336 skipped (flags/unmapped)
Fragments: 31640393 total (31253314 tlen-paired, 2405 hash-paired, 419 singletons, 12178 discordant, 372077 orphans, 7515 too large [>5000 bp], 10067767 duplicates)
Reads: 67120578 total, 37740 skipped (flags/unmapped)
Fragments: 33725567 total (33331171 tlen-paired, 2016 hash-paired, 468 singletons, 8152 discordant, 383760 orphans, 7966 too large [>5000 bp], 10434521 duplicates)
Reads: 72864279 total, 42466 skipped (flags/unmapped)
Fragments: 36614553 total (36156155 tlen-paired, 3328 hash-paired, 348 singletons, 12675 discordant, 442047 orphans, 17551 too large [>5000 bp], 11637777 duplicates)
Reads: 74179826 total, 71462 skipped (flags/unmapped)
Fragments: 37450590 total (36207720 tlen-paired, 2707 hash-paired, 399 singletons, 242323 discordant, 997441 orphans, 102512 too large [>5000 bp], 11891281 duplicates)