Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BVMK-N1-BDNA-1_A23TY32LT4_1/1241_BVMK-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/6511220f1a7552dec39673142cab76/.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/fa/6511220f1a7552dec39673142cab76/.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_BVMK-N1-BDNA-1_A23TY32LT4_1/1241_BVMK-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BVMK-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BVMK-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BVMK-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BVMK-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: 98988471 total, 70063 skipped (flags/unmapped)
Fragments: 49628863 total (49246344 tlen-paired, 5380 hash-paired, 473 singletons, 14957 discordant, 361709 orphans, 11432 too large [>5000 bp], 21095172 duplicates)
Reads: 106864282 total, 60261 skipped (flags/unmapped)
Fragments: 53582031 total (53181036 tlen-paired, 4739 hash-paired, 480 singletons, 10477 discordant, 385299 orphans, 12869 too large [>5000 bp], 22415697 duplicates)
Reads: 117190443 total, 63926 skipped (flags/unmapped)
Fragments: 58763409 total (58299377 tlen-paired, 5071 hash-paired, 402 singletons, 15146 discordant, 443413 orphans, 21757 too large [>5000 bp], 25110182 duplicates)
Reads: 118166539 total, 111684 skipped (flags/unmapped)
Fragments: 59408136 total (58230321 tlen-paired, 4119 hash-paired, 422 singletons, 228283 discordant, 944991 orphans, 91998 too large [>5000 bp], 25355893 duplicates)