Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_2IN-N1-BDNA-1_235YY7LT3_1/1029_2IN-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/60bb5502f7a9b420b43b55dbb563be/.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/9f/60bb5502f7a9b420b43b55dbb563be/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_2IN-N1-BDNA-1_235YY7LT3_1/1029_2IN-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
==> 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_2IN-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2IN-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2IN-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2IN-N1-BDNA-1_235YY7LT3_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: 67030872 total, 57878 skipped (flags/unmapped)
Fragments: 33620067 total (33327970 tlen-paired, 5312 hash-paired, 4377 singletons, 10145 discordant, 272263 orphans, 4750 too large [>5000 bp], 7741279 duplicates)
Reads: 72775395 total, 53486 skipped (flags/unmapped)
Fragments: 36498218 total (36192472 tlen-paired, 4830 hash-paired, 4442 singletons, 7085 discordant, 289389 orphans, 9652 too large [>5000 bp], 8300822 duplicates)
Reads: 74666930 total, 82683 skipped (flags/unmapped)
Fragments: 37575789 total (36702940 tlen-paired, 5943 hash-paired, 4714 singletons, 161741 discordant, 700451 orphans, 68917 too large [>5000 bp], 8574111 duplicates)
Reads: 73998968 total, 55919 skipped (flags/unmapped)
Fragments: 37113083 total (36786688 tlen-paired, 4956 hash-paired, 4631 singletons, 10186 discordant, 306622 orphans, 14068 too large [>5000 bp], 8485526 duplicates)