Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1029_FSS-N1-BDNA-1_A23H3NYLT3_1/1029_FSS-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/3818d664ed5f6071997a4002eabad6/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1029_FSS-N1-BDNA-1_A23H3NYLT3_1/1029_FSS-N1-BDNA-1_A23H3NYLT3_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/c1/3818d664ed5f6071997a4002eabad6/.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_FSS-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FSS-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FSS-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FSS-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: 63056361 total, 47773 skipped (flags/unmapped)
Fragments: 31668634 total (31305508 tlen-paired, 13809 hash-paired, 6128 singletons, 5753 discordant, 337436 orphans, 7442 too large [>5000 bp], 4075537 duplicates)
Reads: 58102136 total, 54615 skipped (flags/unmapped)
Fragments: 29169136 total (28846915 tlen-paired, 12016 hash-paired, 5564 singletons, 5558 discordant, 299083 orphans, 6948 too large [>5000 bp], 3784621 duplicates)
Reads: 62910090 total, 47030 skipped (flags/unmapped)
Fragments: 31601539 total (31228550 tlen-paired, 12347 hash-paired, 6000 singletons, 4670 discordant, 349972 orphans, 7977 too large [>5000 bp], 4067231 duplicates)
Reads: 63746929 total, 79823 skipped (flags/unmapped)
Fragments: 32200260 total (31073430 tlen-paired, 11914 hash-paired, 6109 singletons, 217906 discordant, 890901 orphans, 81798 too large [>5000 bp], 4090772 duplicates)