Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/cf97be07eef2629bbe9ce9a892d315/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_R45-N1-BDNA-1_A23TY7KLT4_1/1241_R45-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/cf97be07eef2629bbe9ce9a892d315/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_R45-N1-BDNA-1_A23TY7KLT4_1/1241_R45-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_R45-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R45-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R45-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R45-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: 78741466 total, 66297 skipped (flags/unmapped)
Fragments: 39469460 total (39171015 tlen-paired, 3069 hash-paired, 312 singletons, 13489 discordant, 281575 orphans, 9068 too large [>5000 bp], 14597498 duplicates)
Reads: 84890588 total, 58876 skipped (flags/unmapped)
Fragments: 42553871 total (42242385 tlen-paired, 3918 hash-paired, 440 singletons, 10370 discordant, 296758 orphans, 10584 too large [>5000 bp], 15360182 duplicates)
Reads: 84026816 total, 61379 skipped (flags/unmapped)
Fragments: 42125422 total (41781345 tlen-paired, 3327 hash-paired, 256 singletons, 12361 discordant, 328133 orphans, 21491 too large [>5000 bp], 15607506 duplicates)
Reads: 93028000 total, 95098 skipped (flags/unmapped)
Fragments: 46736495 total (45892401 tlen-paired, 3001 hash-paired, 323 singletons, 165503 discordant, 675267 orphans, 67751 too large [>5000 bp], 17314308 duplicates)