Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_3FE-N1-BDNA-1_A23H3NYLT3_1/1136_3FE-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/de2bf4fe6ab968b693beffe9ec65dd/.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/84/de2bf4fe6ab968b693beffe9ec65dd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_3FE-N1-BDNA-1_A23H3NYLT3_1/1136_3FE-N1-BDNA-1_A23H3NYLT3_1.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: 1136_3FE-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_3FE-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_3FE-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_3FE-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: 67434374 total, 52403 skipped (flags/unmapped)
Fragments: 33977897 total (33374406 tlen-paired, 5373 hash-paired, 6108 singletons, 5887 discordant, 586123 orphans, 9204 too large [>5000 bp], 4600117 duplicates)
Reads: 67902479 total, 59431 skipped (flags/unmapped)
Fragments: 34196399 total (33615229 tlen-paired, 5704 hash-paired, 6576 singletons, 6636 discordant, 562254 orphans, 9540 too large [>5000 bp], 4658476 duplicates)
Reads: 74480461 total, 54853 skipped (flags/unmapped)
Fragments: 37536108 total (36854523 tlen-paired, 6821 hash-paired, 6843 singletons, 5408 discordant, 662513 orphans, 11374 too large [>5000 bp], 5036586 duplicates)
Reads: 75815525 total, 89844 skipped (flags/unmapped)
Fragments: 38556598 total (36406130 tlen-paired, 5951 hash-paired, 6874 singletons, 434178 discordant, 1703465 orphans, 161412 too large [>5000 bp], 5085927 duplicates)