Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_CI3-N1-BDNA-1_A23TY32LT4_1/1241_CI3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/f3424a93882ec2dc643750abe431ae/.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_CI3-N1-BDNA-1_A23TY32LT4_1/1241_CI3-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/2f/f3424a93882ec2dc643750abe431ae/.command.run
==> 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_CI3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_CI3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_CI3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_CI3-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: 101795395 total, 71008 skipped (flags/unmapped)
Fragments: 51036474 total (50637238 tlen-paired, 4149 hash-paired, 373 singletons, 17962 discordant, 376752 orphans, 14282 too large [>5000 bp], 20300566 duplicates)
Reads: 109387012 total, 62356 skipped (flags/unmapped)
Fragments: 54844197 total (54437661 tlen-paired, 5140 hash-paired, 434 singletons, 12426 discordant, 388536 orphans, 12616 too large [>5000 bp], 21606231 duplicates)
Reads: 121340830 total, 121207 skipped (flags/unmapped)
Fragments: 60983483 total (59825669 tlen-paired, 5952 hash-paired, 474 singletons, 223437 discordant, 927951 orphans, 90541 too large [>5000 bp], 24443523 duplicates)
Reads: 119685577 total, 65525 skipped (flags/unmapped)
Fragments: 60017474 total (59524260 tlen-paired, 4150 hash-paired, 380 singletons, 18956 discordant, 469728 orphans, 27606 too large [>5000 bp], 24076708 duplicates)