Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BGPR-N1-BDNA-1_B23H2GYLT3_1/1029_BGPR-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BGPR-N1-BDNA-1_B23H2GYLT3_1/1029_BGPR-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/cdef5783bf158d0bdb719984087718/.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/2b/cdef5783bf158d0bdb719984087718/.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: 1029_BGPR-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGPR-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGPR-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGPR-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: 113148322 total, 96224 skipped (flags/unmapped)
Fragments: 56772545 total (56222793 tlen-paired, 22332 hash-paired, 9028 singletons, 13102 discordant, 505290 orphans, 10663 too large [>5000 bp], 14503312 duplicates)
Reads: 124084171 total, 83483 skipped (flags/unmapped)
Fragments: 62277422 total (61662886 tlen-paired, 24507 hash-paired, 9622 singletons, 10085 discordant, 570322 orphans, 12894 too large [>5000 bp], 15872544 duplicates)
Reads: 124180093 total, 91467 skipped (flags/unmapped)
Fragments: 62316438 total (61684393 tlen-paired, 26377 hash-paired, 9785 singletons, 13382 discordant, 582501 orphans, 24018 too large [>5000 bp], 15800941 duplicates)
Reads: 126951800 total, 156247 skipped (flags/unmapped)
Fragments: 63980409 total (62169259 tlen-paired, 27564 hash-paired, 10081 singletons, 342481 discordant, 1431024 orphans, 137920 too large [>5000 bp], 16141093 duplicates)