Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/c0afbdec9bca3929827eeec71ba028/.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/39/c0afbdec9bca3929827eeec71ba028/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_7PX-N1-BDNA-1_B23KFG5LT4_1/1136_7PX-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_7PX-N1-BDNA-1_B23KFG5LT4_1/1136_7PX-N1-BDNA-1_B23KFG5LT4_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: 1136_7PX-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7PX-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7PX-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7PX-N1-BDNA-1_B23KFG5LT4_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: 73235589 total, 45625 skipped (flags/unmapped)
Fragments: 36700712 total (36454846 tlen-paired, 2589 hash-paired, 377 singletons, 9947 discordant, 232953 orphans, 10935 too large [>5000 bp], 13657930 duplicates)
Reads: 69454727 total, 57204 skipped (flags/unmapped)
Fragments: 34804550 total (34554429 tlen-paired, 3745 hash-paired, 307 singletons, 14413 discordant, 231656 orphans, 10193 too large [>5000 bp], 13285011 duplicates)
Reads: 81275340 total, 79936 skipped (flags/unmapped)
Fragments: 40804903 total (40177253 tlen-paired, 2704 hash-paired, 301 singletons, 115378 discordant, 509267 orphans, 47583 too large [>5000 bp], 15606404 duplicates)
Reads: 80853342 total, 50352 skipped (flags/unmapped)
Fragments: 40521682 total (40226237 tlen-paired, 8783 hash-paired, 271 singletons, 13862 discordant, 272529 orphans, 16213 too large [>5000 bp], 15466524 duplicates)