Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BA7A-N1-BDNA-1_A23TY7KLT4_1/1241_BA7A-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/e59e7410daacd79f7d18ad534ec9df/.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/1c/e59e7410daacd79f7d18ad534ec9df/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BA7A-N1-BDNA-1_A23TY7KLT4_1/1241_BA7A-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
==> 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_BA7A-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BA7A-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BA7A-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BA7A-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: 85982105 total, 62731 skipped (flags/unmapped)
Fragments: 43057418 total (42827025 tlen-paired, 4006 hash-paired, 306 singletons, 12059 discordant, 214022 orphans, 9433 too large [>5000 bp], 15428508 duplicates)
Reads: 91600087 total, 51576 skipped (flags/unmapped)
Fragments: 45875057 total (45643935 tlen-paired, 3277 hash-paired, 406 singletons, 7980 discordant, 219459 orphans, 9131 too large [>5000 bp], 16213734 duplicates)
Reads: 99917517 total, 58315 skipped (flags/unmapped)
Fragments: 50041265 total (49753094 tlen-paired, 5907 hash-paired, 304 singletons, 12074 discordant, 269886 orphans, 23431 too large [>5000 bp], 18085911 duplicates)
Reads: 100813460 total, 92081 skipped (flags/unmapped)
Fragments: 50557756 total (49944586 tlen-paired, 2651 hash-paired, 403 singletons, 115638 discordant, 494478 orphans, 50374 too large [>5000 bp], 18292625 duplicates)