Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_8B-N1-BDNA-1_B23KGCJLT4_1/1136_8B-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/20b295965ac9daeebe3137445e2643/.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/ba/20b295965ac9daeebe3137445e2643/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_8B-N1-BDNA-1_B23KGCJLT4_1/1136_8B-N1-BDNA-1_B23KGCJLT4_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: 1136_8B-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8B-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8B-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8B-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: 77981431 total, 54664 skipped (flags/unmapped)
Fragments: 39068940 total (38816724 tlen-paired, 3250 hash-paired, 349 singletons, 13971 discordant, 234646 orphans, 11941 too large [>5000 bp], 15143750 duplicates)
Reads: 83519931 total, 46024 skipped (flags/unmapped)
Fragments: 41843562 total (41595038 tlen-paired, 2749 hash-paired, 415 singletons, 9212 discordant, 236148 orphans, 11673 too large [>5000 bp], 15867317 duplicates)
Reads: 91936642 total, 48938 skipped (flags/unmapped)
Fragments: 46069697 total (45767314 tlen-paired, 5951 hash-paired, 318 singletons, 13956 discordant, 282158 orphans, 15393 too large [>5000 bp], 17965899 duplicates)
Reads: 92419677 total, 77452 skipped (flags/unmapped)
Fragments: 46379735 total (45724948 tlen-paired, 3600 hash-paired, 380 singletons, 123186 discordant, 527621 orphans, 55378 too large [>5000 bp], 18096172 duplicates)