Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BEGO-N1-BDNA-1_A23TY7KLT4_1/1241_BEGO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BEGO-N1-BDNA-1_A23TY7KLT4_1/1241_BEGO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/20adf16256b60cfbed1edefcf869aa/.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/ca/20adf16256b60cfbed1edefcf869aa/.command.run
==> 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_BEGO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BEGO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BEGO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BEGO-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: 85518528 total, 56816 skipped (flags/unmapped)
Fragments: 42844505 total (42583417 tlen-paired, 4789 hash-paired, 396 singletons, 11901 discordant, 244002 orphans, 8550 too large [>5000 bp], 14809417 duplicates)
Reads: 92404368 total, 46205 skipped (flags/unmapped)
Fragments: 46297999 total (46031549 tlen-paired, 2059 hash-paired, 402 singletons, 9008 discordant, 254981 orphans, 8774 too large [>5000 bp], 15730362 duplicates)
Reads: 91005807 total, 49734 skipped (flags/unmapped)
Fragments: 45600329 total (45302303 tlen-paired, 3334 hash-paired, 294 singletons, 10621 discordant, 283777 orphans, 19743 too large [>5000 bp], 15836533 duplicates)
Reads: 100123405 total, 81248 skipped (flags/unmapped)
Fragments: 50252461 total (49530381 tlen-paired, 2793 hash-paired, 383 singletons, 139786 discordant, 579118 orphans, 58368 too large [>5000 bp], 17489186 duplicates)