Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_ULB-N1-BDNA-1_A23TY32LT4_1/1241_ULB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/aaa8979074dd76311b0e1b381d5b97/.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/e2/aaa8979074dd76311b0e1b381d5b97/.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_ULB-N1-BDNA-1_A23TY32LT4_1/1241_ULB-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_ULB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_ULB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_ULB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_ULB-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: 83849124 total, 59804 skipped (flags/unmapped)
Fragments: 42023328 total (41728759 tlen-paired, 3641 hash-paired, 314 singletons, 12652 discordant, 277962 orphans, 10470 too large [>5000 bp], 16699421 duplicates)
Reads: 90207987 total, 52429 skipped (flags/unmapped)
Fragments: 45215927 total (44888560 tlen-paired, 4706 hash-paired, 308 singletons, 11311 discordant, 311042 orphans, 17527 too large [>5000 bp], 18071481 duplicates)
Reads: 90661811 total, 51017 skipped (flags/unmapped)
Fragments: 45443240 total (45135148 tlen-paired, 4168 hash-paired, 389 singletons, 8766 discordant, 294769 orphans, 9736 too large [>5000 bp], 17706067 duplicates)
Reads: 99674811 total, 91802 skipped (flags/unmapped)
Fragments: 50066754 total (49207633 tlen-paired, 2740 hash-paired, 352 singletons, 169670 discordant, 686359 orphans, 68106 too large [>5000 bp], 20007887 duplicates)