Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c46fdaf26e579395751fdc784e74d9/.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/2c/c46fdaf26e579395751fdc784e74d9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_1H5-N1-BDNA-1_A23KFG7LT4_1/1136_1H5-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_1H5-N1-BDNA-1_A23KFG7LT4_1/1136_1H5-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_1H5-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_1H5-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_1H5-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1H5-N1-BDNA-1_A23KFG7LT4_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: 75095770 total, 51843 skipped (flags/unmapped)
Fragments: 37641271 total (37363246 tlen-paired, 3770 hash-paired, 401 singletons, 14426 discordant, 259428 orphans, 10607 too large [>5000 bp], 11812801 duplicates)
Reads: 80698212 total, 43652 skipped (flags/unmapped)
Fragments: 40451321 total (40170749 tlen-paired, 3235 hash-paired, 452 singletons, 9223 discordant, 267662 orphans, 10016 too large [>5000 bp], 12436736 duplicates)
Reads: 87419240 total, 46873 skipped (flags/unmapped)
Fragments: 43825194 total (43487302 tlen-paired, 3495 hash-paired, 394 singletons, 15212 discordant, 318791 orphans, 20582 too large [>5000 bp], 13811507 duplicates)
Reads: 88310273 total, 75623 skipped (flags/unmapped)
Fragments: 44363066 total (43606886 tlen-paired, 3074 hash-paired, 395 singletons, 143812 discordant, 608899 orphans, 58906 too large [>5000 bp], 13981684 duplicates)