Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_exw-N1-BDNA-1_A23TY32LT4_1/659_exw-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/76eac60b482f49f3bb99cec14429e2/.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/4f/76eac60b482f49f3bb99cec14429e2/.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_exw-N1-BDNA-1_A23TY32LT4_1/659_exw-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: 659_exw-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_exw-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_exw-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_exw-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: 82385517 total, 65372 skipped (flags/unmapped)
Fragments: 41299408 total (40981426 tlen-paired, 4855 hash-paired, 370 singletons, 13854 discordant, 298903 orphans, 10301 too large [>5000 bp], 15866269 duplicates)
Reads: 88950272 total, 58276 skipped (flags/unmapped)
Fragments: 44597833 total (44223498 tlen-paired, 4879 hash-paired, 301 singletons, 13052 discordant, 356103 orphans, 26367 too large [>5000 bp], 17247240 duplicates)
Reads: 90308154 total, 53706 skipped (flags/unmapped)
Fragments: 45275764 total (44945618 tlen-paired, 3559 hash-paired, 428 singletons, 10075 discordant, 316084 orphans, 9716 too large [>5000 bp], 17096092 duplicates)
Reads: 97977717 total, 103839 skipped (flags/unmapped)
Fragments: 49228552 total (48316764 tlen-paired, 4271 hash-paired, 371 singletons, 180035 discordant, 727111 orphans, 72128 too large [>5000 bp], 19020141 duplicates)