Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_1I1-N1-BDNA-1_A23KFG7LT4_1/1029_1I1-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/25e4906421e568519d5d961be70a0d/.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/f6/25e4906421e568519d5d961be70a0d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_1I1-N1-BDNA-1_A23KFG7LT4_1/1029_1I1-N1-BDNA-1_A23KFG7LT4_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: 1029_1I1-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1I1-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1I1-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1I1-N1-BDNA-1_A23KFG7LT4_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: 73657321 total, 51562 skipped (flags/unmapped)
Fragments: 37057715 total (36515690 tlen-paired, 3029 hash-paired, 392 singletons, 10953 discordant, 527651 orphans, 9186 too large [>5000 bp], 13767698 duplicates)
Reads: 78516618 total, 46493 skipped (flags/unmapped)
Fragments: 39501214 total (38936366 tlen-paired, 2890 hash-paired, 465 singletons, 7953 discordant, 553540 orphans, 10851 too large [>5000 bp], 14300076 duplicates)
Reads: 88783857 total, 79353 skipped (flags/unmapped)
Fragments: 44955283 total (43045974 tlen-paired, 3292 hash-paired, 376 singletons, 383837 discordant, 1521804 orphans, 158059 too large [>5000 bp], 16586334 duplicates)
Reads: 86324327 total, 49954 skipped (flags/unmapped)
Fragments: 43434157 total (42780303 tlen-paired, 3217 hash-paired, 316 singletons, 11558 discordant, 638763 orphans, 22569 too large [>5000 bp], 16171617 duplicates)