Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7FH-N1-BDNA-1_A23NMNVLT4_1/1136_7FH-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/95fbbbe6f3ba5b3536a86b0fda932d/.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/2b/95fbbbe6f3ba5b3536a86b0fda932d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7FH-N1-BDNA-1_A23NMNVLT4_1/1136_7FH-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> 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_7FH-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7FH-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7FH-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7FH-N1-BDNA-1_A23NMNVLT4_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: 67715245 total, 52592 skipped (flags/unmapped)
Fragments: 33929685 total (33704236 tlen-paired, 2281 hash-paired, 332 singletons, 11095 discordant, 211741 orphans, 7678 too large [>5000 bp], 9724093 duplicates)
Reads: 73090024 total, 43448 skipped (flags/unmapped)
Fragments: 36625916 total (36397069 tlen-paired, 1685 hash-paired, 306 singletons, 7624 discordant, 219232 orphans, 7141 too large [>5000 bp], 10280218 duplicates)
Reads: 73069785 total, 46889 skipped (flags/unmapped)
Fragments: 36618747 total (36352502 tlen-paired, 4315 hash-paired, 231 singletons, 9952 discordant, 251747 orphans, 18690 too large [>5000 bp], 10632556 duplicates)
Reads: 80570430 total, 82736 skipped (flags/unmapped)
Fragments: 40442158 total (39817871 tlen-paired, 2841 hash-paired, 374 singletons, 121514 discordant, 499558 orphans, 51655 too large [>5000 bp], 11755208 duplicates)