Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_I78-N1-BDNA-1_235YY7LT3_1/1029_I78-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_I78-N1-BDNA-1_235YY7LT3_1/1029_I78-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/dbc9c831f2438262a1bc8e715b1890/.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/1d/dbc9c831f2438262a1bc8e715b1890/.command.run
==> 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_I78-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I78-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I78-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_I78-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 62153220 total, 50357 skipped (flags/unmapped)
Fragments: 31175292 total (30892412 tlen-paired, 3850 hash-paired, 3162 singletons, 8039 discordant, 267829 orphans, 11635 too large [>5000 bp], 7283513 duplicates)
Reads: 62130561 total, 52400 skipped (flags/unmapped)
Fragments: 31163322 total (30892727 tlen-paired, 3940 hash-paired, 3450 singletons, 9608 discordant, 253597 orphans, 4282 too large [>5000 bp], 7356931 duplicates)
Reads: 67256200 total, 49389 skipped (flags/unmapped)
Fragments: 33732229 total (33446306 tlen-paired, 4625 hash-paired, 3605 singletons, 6649 discordant, 271044 orphans, 8501 too large [>5000 bp], 7826850 duplicates)
Reads: 68761154 total, 77242 skipped (flags/unmapped)
Fragments: 34601589 total (33801029 tlen-paired, 3601 hash-paired, 3744 singletons, 153013 discordant, 640202 orphans, 62340 too large [>5000 bp], 8074460 duplicates)