Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/97287be4b76c4e88986832287f6fea/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_6GU-N1-BDNA-1_A23TY32LT4_1/1241_6GU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  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/b4/97287be4b76c4e88986832287f6fea/.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_6GU-N1-BDNA-1_A23TY32LT4_1/1241_6GU-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] The index file is older than the data file: 1241_6GU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_6GU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_6GU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_6GU-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: 89991093 total, 52028 skipped (flags/unmapped)
Fragments: 45131370 total (44773334 tlen-paired, 2616 hash-paired, 376 singletons, 11101 discordant, 343943 orphans, 10322 too large [>5000 bp], 17880572 duplicates)
Reads: 84089763 total, 62618 skipped (flags/unmapped)
Fragments: 42169219 total (41818488 tlen-paired, 2917 hash-paired, 321 singletons, 15521 discordant, 331972 orphans, 10500 too large [>5000 bp], 16908045 duplicates)
Reads: 99583869 total, 58726 skipped (flags/unmapped)
Fragments: 49940284 total (49529108 tlen-paired, 4950 hash-paired, 342 singletons, 16471 discordant, 389413 orphans, 17165 too large [>5000 bp], 20171195 duplicates)
Reads: 100206533 total, 100230 skipped (flags/unmapped)
Fragments: 50381439 total (49364804 tlen-paired, 3432 hash-paired, 382 singletons, 196216 discordant, 816605 orphans, 80206 too large [>5000 bp], 20325919 duplicates)