Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/628b1ba037d9ba0cd78aba3e1f242d/.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/bd/628b1ba037d9ba0cd78aba3e1f242d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_85T-N1-BDNA-1_B23KGCJLT4_1/1136_85T-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_85T-N1-BDNA-1_B23KGCJLT4_1/1136_85T-N1-BDNA-1_B23KGCJLT4_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_85T-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_85T-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_85T-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_85T-N1-BDNA-1_B23KGCJLT4_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: 83591218 total, 62609 skipped (flags/unmapped)
Fragments: 41910907 total (41566353 tlen-paired, 3578 hash-paired, 449 singletons, 18975 discordant, 321552 orphans, 14398 too large [>5000 bp], 16790526 duplicates)
Reads: 89327725 total, 56247 skipped (flags/unmapped)
Fragments: 44797643 total (44402752 tlen-paired, 5143 hash-paired, 403 singletons, 16756 discordant, 372589 orphans, 24592 too large [>5000 bp], 17989274 duplicates)
Reads: 90161172 total, 52226 skipped (flags/unmapped)
Fragments: 45207125 total (44861973 tlen-paired, 2485 hash-paired, 496 singletons, 13443 discordant, 328728 orphans, 11960 too large [>5000 bp], 17647657 duplicates)
Reads: 98825262 total, 88158 skipped (flags/unmapped)
Fragments: 49653414 total (48765405 tlen-paired, 2893 hash-paired, 432 singletons, 170992 discordant, 713692 orphans, 72200 too large [>5000 bp], 19967091 duplicates)