Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/4815bf656ee69c9450772c871dc170/.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/02/4815bf656ee69c9450772c871dc170/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_BF7W-N1-BDNA-1_A23NMNVLT4_1/1029_BF7W-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_BF7W-N1-BDNA-1_A23NMNVLT4_1/1029_BF7W-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> 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_BF7W-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BF7W-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BF7W-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BF7W-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: 77584363 total, 49248 skipped (flags/unmapped)
Fragments: 38864388 total (38641603 tlen-paired, 3804 hash-paired, 336 singletons, 8300 discordant, 210345 orphans, 8510 too large [>5000 bp], 9928948 duplicates)
Reads: 83144842 total, 41898 skipped (flags/unmapped)
Fragments: 41659678 total (41397716 tlen-paired, 3366 hash-paired, 297 singletons, 7208 discordant, 251091 orphans, 17488 too large [>5000 bp], 10834064 duplicates)
Reads: 84065840 total, 40423 skipped (flags/unmapped)
Fragments: 42117409 total (41885929 tlen-paired, 2533 hash-paired, 398 singletons, 6228 discordant, 222321 orphans, 6659 too large [>5000 bp], 10573099 duplicates)
Reads: 91744903 total, 72709 skipped (flags/unmapped)
Fragments: 46048840 total (45378955 tlen-paired, 2423 hash-paired, 366 singletons, 131976 discordant, 535120 orphans, 55000 too large [>5000 bp], 11993517 duplicates)