Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BXRZ-N1-BDNA-1_A23TY7KLT4_1/1241_BXRZ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/d83ec7bf068b7321e6c700cb50c9ad/.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/3a/d83ec7bf068b7321e6c700cb50c9ad/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BXRZ-N1-BDNA-1_A23TY7KLT4_1/1241_BXRZ-N1-BDNA-1_A23TY7KLT4_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_BXRZ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_BXRZ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_BXRZ-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BXRZ-N1-BDNA-1_A23TY7KLT4_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: 107259875 total, 75079 skipped (flags/unmapped)
Fragments: 53745496 total (53388719 tlen-paired, 3553 hash-paired, 472 singletons, 18350 discordant, 334402 orphans, 14339 too large [>5000 bp], 20774597 duplicates)
Reads: 114196508 total, 62164 skipped (flags/unmapped)
Fragments: 57226429 total (56867774 tlen-paired, 4977 hash-paired, 528 singletons, 12066 discordant, 341084 orphans, 11549 too large [>5000 bp], 21744818 duplicates)
Reads: 124975317 total, 69304 skipped (flags/unmapped)
Fragments: 62631912 total (62199571 tlen-paired, 5088 hash-paired, 430 singletons, 18140 discordant, 408683 orphans, 25651 too large [>5000 bp], 24337833 duplicates)
Reads: 125692311 total, 117367 skipped (flags/unmapped)
Fragments: 63104444 total (62123951 tlen-paired, 5312 hash-paired, 497 singletons, 185535 discordant, 789149 orphans, 77851 too large [>5000 bp], 24539056 duplicates)