Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BG65-N1-BDNA-1_B23L5TMLT4_1/1029_BG65-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BG65-N1-BDNA-1_B23L5TMLT4_1/1029_BG65-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/7311e648cdb5916f89141742359afd/.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/eb/7311e648cdb5916f89141742359afd/.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_BG65-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BG65-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BG65-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BG65-N1-BDNA-1_B23L5TMLT4_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: 118487607 total, 88832 skipped (flags/unmapped)
Fragments: 59527042 total (58808177 tlen-paired, 4327 hash-paired, 638 singletons, 22815 discordant, 691085 orphans, 18207 too large [>5000 bp], 23555075 duplicates)
Reads: 126160757 total, 76866 skipped (flags/unmapped)
Fragments: 63388856 total (62642871 tlen-paired, 5205 hash-paired, 871 singletons, 16119 discordant, 723790 orphans, 15420 too large [>5000 bp], 24674193 duplicates)
Reads: 137466673 total, 82503 skipped (flags/unmapped)
Fragments: 69071327 total (68249675 tlen-paired, 6993 hash-paired, 720 singletons, 22325 discordant, 791614 orphans, 16925 too large [>5000 bp], 27403331 duplicates)
Reads: 139238042 total, 148104 skipped (flags/unmapped)
Fragments: 70289238 total (67962050 tlen-paired, 4444 hash-paired, 749 singletons, 454122 discordant, 1867873 orphans, 190042 too large [>5000 bp], 27728510 duplicates)