Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/565d1221fbb160d9ffc6d9c04a2fd6/.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_BCDN-N1-BDNA-1_A23TY32LT4_1/1241_BCDN-N1-BDNA-1_A23TY32LT4_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/82/565d1221fbb160d9ffc6d9c04a2fd6/.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_BCDN-N1-BDNA-1_A23TY32LT4_1/1241_BCDN-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
==> 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_BCDN-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_BCDN-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BCDN-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BCDN-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: 65880177 total, 38928 skipped (flags/unmapped)
Fragments: 33032459 total (32782612 tlen-paired, 2109 hash-paired, 315 singletons, 7813 discordant, 239610 orphans, 8128 too large [>5000 bp], 11270649 duplicates)
Reads: 60734517 total, 44351 skipped (flags/unmapped)
Fragments: 30453507 total (30210338 tlen-paired, 3033 hash-paired, 304 singletons, 10754 discordant, 229078 orphans, 6267 too large [>5000 bp], 10543241 duplicates)
Reads: 72456743 total, 75476 skipped (flags/unmapped)
Fragments: 36416995 total (35716072 tlen-paired, 2758 hash-paired, 291 singletons, 135724 discordant, 562150 orphans, 54859 too large [>5000 bp], 12655386 duplicates)
Reads: 71801493 total, 42019 skipped (flags/unmapped)
Fragments: 36000618 total (35711326 tlen-paired, 4428 hash-paired, 252 singletons, 11640 discordant, 272972 orphans, 15731 too large [>5000 bp], 12546531 duplicates)