Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/2b466216f6a8aa5a0c57f5c1ca9482/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BHQX-N1-BDNA-1_B23L5TMLT4_1/1029_BHQX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  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/e1/2b466216f6a8aa5a0c57f5c1ca9482/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BHQX-N1-BDNA-1_B23L5TMLT4_1/1029_BHQX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BHQX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BHQX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHQX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHQX-N1-BDNA-1_B23L5TMLT4_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: 87450841 total, 68775 skipped (flags/unmapped)
Fragments: 43886634 total (43450858 tlen-paired, 4948 hash-paired, 557 singletons, 16308 discordant, 413963 orphans, 11659 too large [>5000 bp], 17453031 duplicates)
Reads: 92610441 total, 60749 skipped (flags/unmapped)
Fragments: 46475598 total (46032174 tlen-paired, 4587 hash-paired, 623 singletons, 11347 discordant, 426867 orphans, 12993 too large [>5000 bp], 18212094 duplicates)
Reads: 102805197 total, 105716 skipped (flags/unmapped)
Fragments: 51777400 total (50446859 tlen-paired, 3011 hash-paired, 574 singletons, 257201 discordant, 1069755 orphans, 107505 too large [>5000 bp], 20569480 duplicates)
Reads: 101875614 total, 63877 skipped (flags/unmapped)
Fragments: 51127945 total (50628591 tlen-paired, 4576 hash-paired, 499 singletons, 16319 discordant, 477960 orphans, 17153 too large [>5000 bp], 20385924 duplicates)