Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/14511b3c55abfe2ab41666d12c97c6/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BNKA-N1-BDNA-1_A23TY7KLT4_1/1241_BNKA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  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/19/14511b3c55abfe2ab41666d12c97c6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BNKA-N1-BDNA-1_A23TY7KLT4_1/1241_BNKA-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_BNKA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BNKA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BNKA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BNKA-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: 74955218 total, 54075 skipped (flags/unmapped)
Fragments: 37555361 total (37311005 tlen-paired, 4078 hash-paired, 347 singletons, 10519 discordant, 229412 orphans, 10090 too large [>5000 bp], 12988536 duplicates)
Reads: 80286858 total, 46070 skipped (flags/unmapped)
Fragments: 40229608 total (39981354 tlen-paired, 3391 hash-paired, 367 singletons, 7319 discordant, 237177 orphans, 9558 too large [>5000 bp], 13621148 duplicates)
Reads: 87462908 total, 48552 skipped (flags/unmapped)
Fragments: 43833290 total (43522655 tlen-paired, 3732 hash-paired, 280 singletons, 11063 discordant, 295560 orphans, 21808 too large [>5000 bp], 15166872 duplicates)
Reads: 87887122 total, 81040 skipped (flags/unmapped)
Fragments: 44129793 total (43424707 tlen-paired, 3971 hash-paired, 320 singletons, 134699 discordant, 566096 orphans, 56456 too large [>5000 bp], 15295576 duplicates)