Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/97830cf4897bc0151e26a9355c0a12/.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/72/97830cf4897bc0151e26a9355c0a12/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BHJD-N1-BDNA-1_A23KFG7LT4_1/1029_BHJD-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/1029_BHJD-N1-BDNA-1_A23KFG7LT4_1/1029_BHJD-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: 1029_BHJD-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BHJD-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BHJD-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BHJD-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: 73388212 total, 50195 skipped (flags/unmapped)
Fragments: 36870183 total (36437738 tlen-paired, 2301 hash-paired, 413 singletons, 11491 discordant, 418240 orphans, 8152 too large [>5000 bp], 13239177 duplicates)
Reads: 77849903 total, 42691 skipped (flags/unmapped)
Fragments: 39114847 total (38667163 tlen-paired, 1860 hash-paired, 382 singletons, 8188 discordant, 437254 orphans, 7577 too large [>5000 bp], 13672227 duplicates)
Reads: 85747744 total, 45977 skipped (flags/unmapped)
Fragments: 43081528 total (42560562 tlen-paired, 3573 hash-paired, 395 singletons, 12178 discordant, 504820 orphans, 21963 too large [>5000 bp], 15505026 duplicates)
Reads: 87406110 total, 79245 skipped (flags/unmapped)
Fragments: 44127333 total (42671726 tlen-paired, 1571 hash-paired, 445 singletons, 288661 discordant, 1164930 orphans, 118787 too large [>5000 bp], 15809571 duplicates)