Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/d1b53b28e23600d9a2bd79e68f0d08/.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/a3/d1b53b28e23600d9a2bd79e68f0d08/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_0T4-N1-BDNA-1_A23H3W5LT3_1/1136_0T4-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_0T4-N1-BDNA-1_A23H3W5LT3_1/1136_0T4-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
==> 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: 1136_0T4-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0T4-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0T4-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0T4-N1-BDNA-1_A23H3W5LT3_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: 78507873 total, 70812 skipped (flags/unmapped)
Fragments: 39361855 total (39038398 tlen-paired, 10406 hash-paired, 4887 singletons, 8824 discordant, 299340 orphans, 8789 too large [>5000 bp], 8041370 duplicates)
Reads: 85464459 total, 62462 skipped (flags/unmapped)
Fragments: 42863702 total (42504337 tlen-paired, 10860 hash-paired, 5283 singletons, 6184 discordant, 337038 orphans, 8457 too large [>5000 bp], 8740035 duplicates)
Reads: 86317847 total, 65479 skipped (flags/unmapped)
Fragments: 43290002 total (42914679 tlen-paired, 12611 hash-paired, 5377 singletons, 8624 discordant, 348711 orphans, 13226 too large [>5000 bp], 8809285 duplicates)
Reads: 87972704 total, 110285 skipped (flags/unmapped)
Fragments: 44274185 total (43211142 tlen-paired, 11631 hash-paired, 5554 singletons, 203545 discordant, 842313 orphans, 80958 too large [>5000 bp], 8938931 duplicates)