Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_D5-N1-BDNA-1_B23L5TMLT4_1/1047_D5-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/4195b52d5b018df0825155672e181a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_D5-N1-BDNA-1_B23L5TMLT4_1/1047_D5-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  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/d5/4195b52d5b018df0825155672e181a/.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: 1047_D5-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_D5-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_D5-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_D5-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: 44001044 total, 36141 skipped (flags/unmapped)
Fragments: 22137231 total (21803792 tlen-paired, 2328 hash-paired, 235 singletons, 5882 discordant, 324994 orphans, 7835 too large [>5000 bp], 7444903 duplicates)
Reads: 46096145 total, 30541 skipped (flags/unmapped)
Fragments: 23202190 total (22826468 tlen-paired, 3988 hash-paired, 222 singletons, 5760 discordant, 365752 orphans, 13599 too large [>5000 bp], 7789468 duplicates)
Reads: 46958598 total, 29746 skipped (flags/unmapped)
Fragments: 23634420 total (23274167 tlen-paired, 2003 hash-paired, 312 singletons, 4184 discordant, 353754 orphans, 7039 too large [>5000 bp], 7737817 duplicates)
Reads: 51825180 total, 57234 skipped (flags/unmapped)
Fragments: 26254342 total (25074998 tlen-paired, 2011 hash-paired, 278 singletons, 240265 discordant, 936790 orphans, 98165 too large [>5000 bp], 8703548 duplicates)