Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/e7cfc588303f02275b97ce9dc9141b/.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/49/e7cfc588303f02275b97ce9dc9141b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_MH0-N1-BDNA-1_B23H2GYLT3_1/1029_MH0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_MH0-N1-BDNA-1_B23H2GYLT3_1/1029_MH0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
==> 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_MH0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MH0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MH0-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MH0-N1-BDNA-1_B23H2GYLT3_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: 77697671 total, 68173 skipped (flags/unmapped)
Fragments: 39012584 total (38582349 tlen-paired, 10348 hash-paired, 6360 singletons, 9045 discordant, 404482 orphans, 7586 too large [>5000 bp], 7988365 duplicates)
Reads: 86036490 total, 60733 skipped (flags/unmapped)
Fragments: 43211511 total (42728056 tlen-paired, 10761 hash-paired, 6874 singletons, 8363 discordant, 457457 orphans, 8533 too large [>5000 bp], 8800841 duplicates)
Reads: 85539098 total, 59130 skipped (flags/unmapped)
Fragments: 42968247 total (42476735 tlen-paired, 11943 hash-paired, 6875 singletons, 6179 discordant, 466515 orphans, 8432 too large [>5000 bp], 8794456 duplicates)
Reads: 87712966 total, 106421 skipped (flags/unmapped)
Fragments: 44295857 total (42785530 tlen-paired, 11794 hash-paired, 7111 singletons, 291322 discordant, 1200100 orphans, 111021 too large [>5000 bp], 8912075 duplicates)