Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/9197b1c31efb01be4c7ada27aa87d9/.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/9d/9197b1c31efb01be4c7ada27aa87d9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_JU5-N1-BDNA-1_A23NMNVLT4_1/1029_JU5-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_JU5-N1-BDNA-1_A23NMNVLT4_1/1029_JU5-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: 1029_JU5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_JU5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_JU5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_JU5-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: 79029348 total, 57989 skipped (flags/unmapped)
Fragments: 39589651 total (39346914 tlen-paired, 3320 hash-paired, 324 singletons, 12904 discordant, 226189 orphans, 9285 too large [>5000 bp], 11786366 duplicates)
Reads: 85140912 total, 47509 skipped (flags/unmapped)
Fragments: 42652776 total (42412953 tlen-paired, 2135 hash-paired, 311 singletons, 8853 discordant, 228524 orphans, 8343 too large [>5000 bp], 12523887 duplicates)
Reads: 85335034 total, 51438 skipped (flags/unmapped)
Fragments: 42753932 total (42473317 tlen-paired, 5644 hash-paired, 271 singletons, 11477 discordant, 263223 orphans, 19613 too large [>5000 bp], 12898461 duplicates)
Reads: 93490332 total, 82733 skipped (flags/unmapped)
Fragments: 46907212 total (46273006 tlen-paired, 1846 hash-paired, 395 singletons, 122277 discordant, 509688 orphans, 51629 too large [>5000 bp], 14173093 duplicates)