Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BTAF-N1-BDNA-1_B23L5TMLT4_1/1029_BTAF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/4977a20acf3aa2f46e1d92e5a05fe1/.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/50/4977a20acf3aa2f46e1d92e5a05fe1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BTAF-N1-BDNA-1_B23L5TMLT4_1/1029_BTAF-N1-BDNA-1_B23L5TMLT4_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: 1029_BTAF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BTAF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BTAF-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BTAF-N1-BDNA-1_B23L5TMLT4_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: 86027516 total, 65374 skipped (flags/unmapped)
Fragments: 43186012 total (42732555 tlen-paired, 4903 hash-paired, 543 singletons, 16168 discordant, 431843 orphans, 11252 too large [>5000 bp], 15193986 duplicates)
Reads: 92040036 total, 57517 skipped (flags/unmapped)
Fragments: 46203380 total (45740250 tlen-paired, 4204 hash-paired, 609 singletons, 11069 discordant, 447248 orphans, 11808 too large [>5000 bp], 15916173 duplicates)
Reads: 99719281 total, 62317 skipped (flags/unmapped)
Fragments: 50056240 total (49546344 tlen-paired, 4040 hash-paired, 482 singletons, 15722 discordant, 489652 orphans, 17309 too large [>5000 bp], 17619089 duplicates)
Reads: 100969311 total, 103917 skipped (flags/unmapped)
Fragments: 50883774 total (49481518 tlen-paired, 4098 hash-paired, 539 singletons, 272282 discordant, 1125337 orphans, 111861 too large [>5000 bp], 17824639 duplicates)