Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/89be2213c1e19534cc86d14906069f/.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/af/89be2213c1e19534cc86d14906069f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BAT5-N1-BDNA-1_A23TY32LT4_1/1241_BAT5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BAT5-N1-BDNA-1_A23TY32LT4_1/1241_BAT5-N1-BDNA-1_A23TY32LT4_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: 1241_BAT5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_BAT5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BAT5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BAT5-N1-BDNA-1_A23TY32LT4_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: 71059087 total, 56744 skipped (flags/unmapped)
Fragments: 35634712 total (35333623 tlen-paired, 4253 hash-paired, 308 singletons, 10669 discordant, 285859 orphans, 9543 too large [>5000 bp], 14341241 duplicates)
Reads: 75665546 total, 45191 skipped (flags/unmapped)
Fragments: 37954265 total (37638180 tlen-paired, 2956 hash-paired, 405 singletons, 7232 discordant, 305492 orphans, 8861 too large [>5000 bp], 14979990 duplicates)
Reads: 84062274 total, 85931 skipped (flags/unmapped)
Fragments: 42293905 total (41340580 tlen-paired, 3837 hash-paired, 294 singletons, 186121 discordant, 763073 orphans, 75950 too large [>5000 bp], 17027418 duplicates)
Reads: 83699937 total, 48203 skipped (flags/unmapped)
Fragments: 41982422 total (41609468 tlen-paired, 3112 hash-paired, 276 singletons, 10640 discordant, 358926 orphans, 23046 too large [>5000 bp], 16952640 duplicates)