Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_b2G-N1-BDNA-1_A23TY32LT4_1/659_b2G-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/5f905a724c6cebb36efdbf287b24c7/.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/c0/5f905a724c6cebb36efdbf287b24c7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_b2G-N1-BDNA-1_A23TY32LT4_1/659_b2G-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: 659_b2G-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b2G-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b2G-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b2G-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 85495472 total, 66951 skipped (flags/unmapped)
Fragments: 42864176 total (42521860 tlen-paired, 3586 hash-paired, 388 singletons, 14523 discordant, 323819 orphans, 12188 too large [>5000 bp], 17055319 duplicates)
Reads: 92253571 total, 59439 skipped (flags/unmapped)
Fragments: 46254524 total (45868503 tlen-paired, 5867 hash-paired, 315 singletons, 13030 discordant, 366809 orphans, 26104 too large [>5000 bp], 18532269 duplicates)
Reads: 93917556 total, 54506 skipped (flags/unmapped)
Fragments: 47096364 total (46735138 tlen-paired, 3611 hash-paired, 402 singletons, 10321 discordant, 346892 orphans, 8808 too large [>5000 bp], 18414944 duplicates)
Reads: 101696789 total, 103491 skipped (flags/unmapped)
Fragments: 51121501 total (50105789 tlen-paired, 4581 hash-paired, 365 singletons, 201973 discordant, 808793 orphans, 79727 too large [>5000 bp], 20450413 duplicates)