Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_B1C-N1-BDNA-1_B23H2GYLT3_1/1029_B1C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/2aa774b27aea0bc8b5eb199a121f83/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_B1C-N1-BDNA-1_B23H2GYLT3_1/1029_B1C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  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/95/2aa774b27aea0bc8b5eb199a121f83/.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_B1C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_B1C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1029_B1C-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_B1C-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: 94877724 total, 84115 skipped (flags/unmapped)
Fragments: 47615954 total (47125317 tlen-paired, 19704 hash-paired, 7174 singletons, 10010 discordant, 453749 orphans, 11312 too large [>5000 bp], 10592020 duplicates)
Reads: 95471169 total, 69863 skipped (flags/unmapped)
Fragments: 47930738 total (47417495 tlen-paired, 20657 hash-paired, 7196 singletons, 8654 discordant, 476736 orphans, 11881 too large [>5000 bp], 10614669 duplicates)
Reads: 106753146 total, 123960 skipped (flags/unmapped)
Fragments: 53841447 total (52185394 tlen-paired, 20770 hash-paired, 8128 singletons, 325915 discordant, 1301240 orphans, 127830 too large [>5000 bp], 11818854 duplicates)
Reads: 104390608 total, 69456 skipped (flags/unmapped)
Fragments: 52414840 total (51858515 tlen-paired, 20619 hash-paired, 7898 singletons, 7424 discordant, 520384 orphans, 9877 too large [>5000 bp], 11627226 duplicates)