Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_X7N-N1-BDNA-1_A23TY7KLT4_1/1241_X7N-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/0751f056c4a2e554f6797fec855617/.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/4d/0751f056c4a2e554f6797fec855617/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_X7N-N1-BDNA-1_A23TY7KLT4_1/1241_X7N-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_X7N-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_X7N-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_X7N-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_X7N-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: 97010768 total, 66642 skipped (flags/unmapped)
Fragments: 48608426 total (48294304 tlen-paired, 4815 hash-paired, 374 singletons, 16755 discordant, 292178 orphans, 9913 too large [>5000 bp], 17594764 duplicates)
Reads: 104986788 total, 54040 skipped (flags/unmapped)
Fragments: 52607308 total (52287076 tlen-paired, 4411 hash-paired, 500 singletons, 12157 discordant, 303164 orphans, 10898 too large [>5000 bp], 18759391 duplicates)
Reads: 103153262 total, 57734 skipped (flags/unmapped)
Fragments: 51691666 total (51332477 tlen-paired, 6564 hash-paired, 348 singletons, 14819 discordant, 337458 orphans, 25001 too large [>5000 bp], 18885070 duplicates)
Reads: 113859029 total, 102358 skipped (flags/unmapped)
Fragments: 57141198 total (56326698 tlen-paired, 4134 hash-paired, 451 singletons, 156523 discordant, 653392 orphans, 64059 too large [>5000 bp], 20898767 duplicates)