Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_451-N1-BDNA-1_A23NMNVLT4_1/1136_451-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/554323126f9bcf992c9613a00ae65b/.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/5b/554323126f9bcf992c9613a00ae65b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_451-N1-BDNA-1_A23NMNVLT4_1/1136_451-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_451-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_451-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_451-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_451-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: 71956523 total, 57308 skipped (flags/unmapped)
Fragments: 36039304 total (35835338 tlen-paired, 3445 hash-paired, 233 singletons, 8948 discordant, 191340 orphans, 6090 too large [>5000 bp], 11427400 duplicates)
Reads: 77005690 total, 46369 skipped (flags/unmapped)
Fragments: 38571741 total (38364979 tlen-paired, 2180 hash-paired, 365 singletons, 5819 discordant, 198398 orphans, 7301 too large [>5000 bp], 12053664 duplicates)
Reads: 85590935 total, 83946 skipped (flags/unmapped)
Fragments: 42944005 total (42348838 tlen-paired, 1902 hash-paired, 322 singletons, 114992 discordant, 477951 orphans, 48626 too large [>5000 bp], 13796391 duplicates)
Reads: 85400932 total, 51134 skipped (flags/unmapped)
Fragments: 42779764 total (42533289 tlen-paired, 2628 hash-paired, 239 singletons, 8559 discordant, 235049 orphans, 12779 too large [>5000 bp], 13719860 duplicates)