Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/cdb313db370302ed4371056d68091d/.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/f6/cdb313db370302ed4371056d68091d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_0EH-N1-BDNA-1_A23H3W5LT3_1/1136_0EH-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_0EH-N1-BDNA-1_A23H3W5LT3_1/1136_0EH-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_0EH-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0EH-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0EH-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0EH-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: 51734458 total, 41454 skipped (flags/unmapped)
Fragments: 26059296 total (25599540 tlen-paired, 3886 hash-paired, 3465 singletons, 4870 discordant, 447535 orphans, 12706 too large [>5000 bp], 4747966 duplicates)
Reads: 51497409 total, 48387 skipped (flags/unmapped)
Fragments: 25927214 total (25501884 tlen-paired, 3153 hash-paired, 3541 singletons, 5451 discordant, 413185 orphans, 5660 too large [>5000 bp], 4759849 duplicates)
Reads: 56390825 total, 42260 skipped (flags/unmapped)
Fragments: 28407690 total (27920455 tlen-paired, 3146 hash-paired, 3749 singletons, 4284 discordant, 476056 orphans, 6495 too large [>5000 bp], 5173385 duplicates)
Reads: 58686178 total, 72883 skipped (flags/unmapped)
Fragments: 29807234 total (28245191 tlen-paired, 3452 hash-paired, 3897 singletons, 315312 discordant, 1239382 orphans, 121053 too large [>5000 bp], 5316327 duplicates)