Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/d6f76c96100664616c40ed163b8242/.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/f6/d6f76c96100664616c40ed163b8242/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_3GP-N1-BDNA-1_A23TY32LT4_1/1241_3GP-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_3GP-N1-BDNA-1_A23TY32LT4_1/1241_3GP-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_3GP-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_3GP-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3GP-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3GP-N1-BDNA-1_A23TY32LT4_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: 84178377 total, 63952 skipped (flags/unmapped)
Fragments: 42200339 total (41869264 tlen-paired, 3525 hash-paired, 319 singletons, 15829 discordant, 311402 orphans, 12734 too large [>5000 bp], 16026530 duplicates)
Reads: 90322388 total, 55336 skipped (flags/unmapped)
Fragments: 45284938 total (44947082 tlen-paired, 3907 hash-paired, 382 singletons, 10287 discordant, 323280 orphans, 10419 too large [>5000 bp], 16961788 duplicates)
Reads: 100284106 total, 104194 skipped (flags/unmapped)
Fragments: 50394796 total (49452951 tlen-paired, 3854 hash-paired, 371 singletons, 180639 discordant, 756981 orphans, 73836 too large [>5000 bp], 19228515 duplicates)
Reads: 99132008 total, 60241 skipped (flags/unmapped)
Fragments: 49699304 total (49302378 tlen-paired, 4267 hash-paired, 359 singletons, 16124 discordant, 376176 orphans, 24847 too large [>5000 bp], 18988839 duplicates)