Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BPR7-N1-BDNA-1_A23TY7KLT4_1/1241_BPR7-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/849d8894169a571283a21f12ef768e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BPR7-N1-BDNA-1_A23TY7KLT4_1/1241_BPR7-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  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/dc/849d8894169a571283a21f12ef768e/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BPR7-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BPR7-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BPR7-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BPR7-N1-BDNA-1_A23TY7KLT4_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: 90227306 total, 63955 skipped (flags/unmapped)
Fragments: 45199143 total (44927046 tlen-paired, 2688 hash-paired, 389 singletons, 12988 discordant, 256032 orphans, 10743 too large [>5000 bp], 16072912 duplicates)
Reads: 97039029 total, 53521 skipped (flags/unmapped)
Fragments: 48615827 total (48334631 tlen-paired, 4392 hash-paired, 480 singletons, 9572 discordant, 266752 orphans, 10543 too large [>5000 bp], 16966592 duplicates)
Reads: 96166827 total, 56437 skipped (flags/unmapped)
Fragments: 48183777 total (47862697 tlen-paired, 4669 hash-paired, 337 singletons, 12079 discordant, 303995 orphans, 23584 too large [>5000 bp], 17214213 duplicates)
Reads: 105782454 total, 95279 skipped (flags/unmapped)
Fragments: 53078658 total (52336398 tlen-paired, 4148 hash-paired, 417 singletons, 143151 discordant, 594544 orphans, 62410 too large [>5000 bp], 19022373 duplicates)