Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/749fa5a7db6b461b80be27b78bfef6/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_02C-N1-BDNA-1_B23KFG5LT4_1/1136_02C-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  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/96/749fa5a7db6b461b80be27b78bfef6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_02C-N1-BDNA-1_B23KFG5LT4_1/1136_02C-N1-BDNA-1_B23KFG5LT4_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: 1136_02C-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_02C-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_02C-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_02C-N1-BDNA-1_B23KFG5LT4_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: 79342318 total, 60934 skipped (flags/unmapped)
Fragments: 39784971 total (39448012 tlen-paired, 3824 hash-paired, 415 singletons, 18563 discordant, 314157 orphans, 13007 too large [>5000 bp], 17059603 duplicates)
Reads: 85035234 total, 48258 skipped (flags/unmapped)
Fragments: 42646019 total (42303488 tlen-paired, 1807 hash-paired, 400 singletons, 13710 discordant, 326614 orphans, 10976 too large [>5000 bp], 17740991 duplicates)
Reads: 85661480 total, 54620 skipped (flags/unmapped)
Fragments: 42961265 total (42582945 tlen-paired, 2660 hash-paired, 317 singletons, 15550 discordant, 359793 orphans, 22220 too large [>5000 bp], 18451456 duplicates)
Reads: 94380451 total, 85084 skipped (flags/unmapped)
Fragments: 47432765 total (46546474 tlen-paired, 3107 hash-paired, 379 singletons, 171765 discordant, 711040 orphans, 70628 too large [>5000 bp], 20422257 duplicates)