Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_2YW-N1-BDNA-1_A23NMNVLT4_1/1136_2YW-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/d3414df94d2d7154359fb54940040d/.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/67/d3414df94d2d7154359fb54940040d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_2YW-N1-BDNA-1_A23NMNVLT4_1/1136_2YW-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: 1136_2YW-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2YW-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2YW-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2YW-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: 57651960 total, 44433 skipped (flags/unmapped)
Fragments: 28890607 total (28692191 tlen-paired, 2592 hash-paired, 259 singletons, 9763 discordant, 185802 orphans, 6187 too large [>5000 bp], 7955149 duplicates)
Reads: 62716184 total, 39800 skipped (flags/unmapped)
Fragments: 31433144 total (31198140 tlen-paired, 2710 hash-paired, 234 singletons, 9204 discordant, 222856 orphans, 16593 too large [>5000 bp], 8768423 duplicates)
Reads: 62766216 total, 38728 skipped (flags/unmapped)
Fragments: 31452809 total (31250839 tlen-paired, 2403 hash-paired, 256 singletons, 6993 discordant, 192318 orphans, 7222 too large [>5000 bp], 8535106 duplicates)
Reads: 68735999 total, 67312 skipped (flags/unmapped)
Fragments: 34507831 total (33968031 tlen-paired, 2299 hash-paired, 309 singletons, 104502 discordant, 432690 orphans, 43012 too large [>5000 bp], 9651615 duplicates)