Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_5O3-N1-BDNA-1_2375WFLT3_s15/1029_5O3-N1-BDNA-1_2375WFLT3_s15.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/73ace9b1129c774007ceff258eef2c/.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/da/73ace9b1129c774007ceff258eef2c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_5O3-N1-BDNA-1_2375WFLT3_s15/1029_5O3-N1-BDNA-1_2375WFLT3_s15.recalibrated.bam.bai
==> 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_5O3-N1-BDNA-1_2375WFLT3_s15.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5O3-N1-BDNA-1_2375WFLT3_s15.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5O3-N1-BDNA-1_2375WFLT3_s15.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5O3-N1-BDNA-1_2375WFLT3_s15.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: 71348192 total, 63349 skipped (flags/unmapped)
Fragments: 35851817 total (35403663 tlen-paired, 4184 hash-paired, 1277 singletons, 14043 discordant, 428650 orphans, 5568 too large [>5000 bp], 10367935 duplicates)
Reads: 77066336 total, 56177 skipped (flags/unmapped)
Fragments: 38726303 total (38254265 tlen-paired, 2945 hash-paired, 1334 singletons, 9856 discordant, 457903 orphans, 8395 too large [>5000 bp], 11025561 duplicates)
Reads: 78837721 total, 59872 skipped (flags/unmapped)
Fragments: 39610613 total (39115025 tlen-paired, 3869 hash-paired, 1347 singletons, 13616 discordant, 476756 orphans, 17363 too large [>5000 bp], 11328811 duplicates)
Reads: 80426812 total, 107891 skipped (flags/unmapped)
Fragments: 40623010 total (39194878 tlen-paired, 3232 hash-paired, 1417 singletons, 273585 discordant, 1149898 orphans, 112108 too large [>5000 bp], 11551473 duplicates)