Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/6059bfae5df44c0fec3ab422b08ab9/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_3Y-N1-BDNA-1_B23H3Y2LT3_1/869_3Y-N1-BDNA-1_B23H3Y2LT3_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/d5/6059bfae5df44c0fec3ab422b08ab9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_3Y-N1-BDNA-1_B23H3Y2LT3_1/869_3Y-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
==> 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: 869_3Y-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
The index file is older than the data file: 869_3Y-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_3Y-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_3Y-N1-BDNA-1_B23H3Y2LT3_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: 94678143 total, 95178 skipped (flags/unmapped)
Fragments: 47579409 total (46953969 tlen-paired, 14578 hash-paired, 2878 singletons, 10619 discordant, 597365 orphans, 12195 too large [>5000 bp], 10859973 duplicates)
Reads: 103413502 total, 79659 skipped (flags/unmapped)
Fragments: 51988965 total (51299117 tlen-paired, 15841 hash-paired, 3264 singletons, 7300 discordant, 663443 orphans, 11310 too large [>5000 bp], 11830916 duplicates)
Reads: 103576783 total, 81590 skipped (flags/unmapped)
Fragments: 52072211 total (51363642 tlen-paired, 15319 hash-paired, 3152 singletons, 10825 discordant, 679273 orphans, 16598 too large [>5000 bp], 11801983 duplicates)
Reads: 107147418 total, 203751 skipped (flags/unmapped)
Fragments: 54184202 total (51971767 tlen-paired, 16747 hash-paired, 3350 singletons, 428733 discordant, 1763605 orphans, 171109 too large [>5000 bp], 12120473 duplicates)