Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/83dabc7f4dbc3964dd976d99e5c72b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_6K1-N1-BDNA-1_A23NMNVLT4_1/1136_6K1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  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/f4/83dabc7f4dbc3964dd976d99e5c72b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_6K1-N1-BDNA-1_A23NMNVLT4_1/1136_6K1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6K1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6K1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6K1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6K1-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: 44743070 total, 30637 skipped (flags/unmapped)
Fragments: 22417373 total (22278290 tlen-paired, 2298 hash-paired, 207 singletons, 5434 discordant, 131144 orphans, 4519 too large [>5000 bp], 5949776 duplicates)
Reads: 48276306 total, 25578 skipped (flags/unmapped)
Fragments: 24189008 total (24047635 tlen-paired, 1320 hash-paired, 246 singletons, 3597 discordant, 136210 orphans, 4584 too large [>5000 bp], 6258402 duplicates)
Reads: 52753306 total, 27409 skipped (flags/unmapped)
Fragments: 26435145 total (26264677 tlen-paired, 1666 hash-paired, 178 singletons, 5581 discordant, 163043 orphans, 9414 too large [>5000 bp], 7056504 duplicates)
Reads: 53161103 total, 43324 skipped (flags/unmapped)
Fragments: 26694531 total (26271988 tlen-paired, 1644 hash-paired, 205 singletons, 82032 discordant, 338662 orphans, 33792 too large [>5000 bp], 7129785 duplicates)