Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_814-N1-BDNA-1_A23H3NYLT3_1/1136_814-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/eecb046b3e0781c3bb5144950820d6/.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/8a/eecb046b3e0781c3bb5144950820d6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_814-N1-BDNA-1_A23H3NYLT3_1/1136_814-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_814-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_814-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_814-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_814-N1-BDNA-1_A23H3NYLT3_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: 96180113 total, 83128 skipped (flags/unmapped)
Fragments: 48344969 total (47707835 tlen-paired, 14939 hash-paired, 9333 singletons, 10028 discordant, 602834 orphans, 9607 too large [>5000 bp], 8316304 duplicates)
Reads: 104827857 total, 74031 skipped (flags/unmapped)
Fragments: 52719047 total (51985312 tlen-paired, 16025 hash-paired, 10073 singletons, 8010 discordant, 699627 orphans, 12716 too large [>5000 bp], 8965987 duplicates)
Reads: 104360520 total, 78767 skipped (flags/unmapped)
Fragments: 52470929 total (51739635 tlen-paired, 16089 hash-paired, 10061 singletons, 10262 discordant, 694882 orphans, 22419 too large [>5000 bp], 8934593 duplicates)
Reads: 106150383 total, 125910 skipped (flags/unmapped)
Fragments: 53756018 total (51479336 tlen-paired, 14340 hash-paired, 10182 singletons, 442905 discordant, 1809255 orphans, 165937 too large [>5000 bp], 9024698 duplicates)