Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_2LI-N1-BDNA-1_235YY7LT3_1/1029_2LI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/7409f6e927cfe5b4f6f9b2a84378c9/.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/77/7409f6e927cfe5b4f6f9b2a84378c9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_2LI-N1-BDNA-1_235YY7LT3_1/1029_2LI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_2LI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
The index file is older than the data file: 1029_2LI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2LI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2LI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 45258111 total, 43166 skipped (flags/unmapped)
Fragments: 22899264 total (22301703 tlen-paired, 2412 hash-paired, 2418 singletons, 4958 discordant, 587773 orphans, 3304 too large [>5000 bp], 5738126 duplicates)
Reads: 48963050 total, 43270 skipped (flags/unmapped)
Fragments: 24783794 total (24117596 tlen-paired, 2083 hash-paired, 2539 singletons, 3809 discordant, 657767 orphans, 6249 too large [>5000 bp], 6011765 duplicates)
Reads: 50110546 total, 44640 skipped (flags/unmapped)
Fragments: 25359043 total (24669507 tlen-paired, 2673 hash-paired, 2626 singletons, 5471 discordant, 678766 orphans, 14606 too large [>5000 bp], 6249149 duplicates)
Reads: 52299084 total, 70962 skipped (flags/unmapped)
Fragments: 26852107 total (24563076 tlen-paired, 2845 hash-paired, 2692 singletons, 448658 discordant, 1834836 orphans, 180718 too large [>5000 bp], 6384207 duplicates)