Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BCD2-N1-BDNA-1_A23TY32LT4_1/1241_BCD2-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/34df29228148572ccbc629ad8d1db8/.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/e4/34df29228148572ccbc629ad8d1db8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BCD2-N1-BDNA-1_A23TY32LT4_1/1241_BCD2-N1-BDNA-1_A23TY32LT4_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: 1241_BCD2-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BCD2-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BCD2-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BCD2-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: 92750977 total, 71739 skipped (flags/unmapped)
Fragments: 46499076 total (46132175 tlen-paired, 4728 hash-paired, 428 singletons, 17651 discordant, 344094 orphans, 12804 too large [>5000 bp], 18431509 duplicates)
Reads: 99896256 total, 61280 skipped (flags/unmapped)
Fragments: 50085195 total (49709452 tlen-paired, 4103 hash-paired, 469 singletons, 12508 discordant, 358663 orphans, 11859 too large [>5000 bp], 19490402 duplicates)
Reads: 99319751 total, 65269 skipped (flags/unmapped)
Fragments: 49800161 total (49389387 tlen-paired, 5571 hash-paired, 385 singletons, 15153 discordant, 389665 orphans, 22105 too large [>5000 bp], 19814115 duplicates)
Reads: 109855911 total, 109715 skipped (flags/unmapped)
Fragments: 55202151 total (54177764 tlen-paired, 4170 hash-paired, 458 singletons, 201651 discordant, 818108 orphans, 80230 too large [>5000 bp], 21945558 duplicates)