Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_JHS-N1-BDNA-1_A23TY32LT4_1/1241_JHS-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/df21bacf6767be07767abb74a0472c/.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/9b/df21bacf6767be07767abb74a0472c/.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_JHS-N1-BDNA-1_A23TY32LT4_1/1241_JHS-N1-BDNA-1_A23TY32LT4_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: 1241_JHS-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_JHS-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_JHS-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_JHS-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: 94650921 total, 69378 skipped (flags/unmapped)
Fragments: 47455545 total (47084121 tlen-paired, 3960 hash-paired, 464 singletons, 14319 discordant, 352681 orphans, 11799 too large [>5000 bp], 19853313 duplicates)
Reads: 102222313 total, 61289 skipped (flags/unmapped)
Fragments: 51257298 total (50866304 tlen-paired, 3974 hash-paired, 516 singletons, 9850 discordant, 376654 orphans, 11799 too large [>5000 bp], 21123997 duplicates)
Reads: 113234673 total, 116100 skipped (flags/unmapped)
Fragments: 56930475 total (55778824 tlen-paired, 4599 hash-paired, 419 singletons, 224757 discordant, 921876 orphans, 89959 too large [>5000 bp], 23951709 duplicates)
Reads: 112170891 total, 64878 skipped (flags/unmapped)
Fragments: 56247229 total (55782431 tlen-paired, 5206 hash-paired, 395 singletons, 15605 discordant, 443592 orphans, 27771 too large [>5000 bp], 23663547 duplicates)