Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/7bbf0b39c720290d313c942857c044/.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/27/7bbf0b39c720290d313c942857c044/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_5OZ-N1-BDNA-1_B23L5TMLT4_1/1136_5OZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_5OZ-N1-BDNA-1_B23L5TMLT4_1/1136_5OZ-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] The index file is older than the data file: 1136_5OZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5OZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5OZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5OZ-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: 32394850 total, 38425 skipped (flags/unmapped)
Fragments: 16668924 total (15672022 tlen-paired, 2895 hash-paired, 192 singletons, 2848 discordant, 990967 orphans, 4868 too large [>5000 bp], 6787525 duplicates)
Reads: 34300516 total, 35515 skipped (flags/unmapped)
Fragments: 17650773 total (16590375 tlen-paired, 4386 hash-paired, 167 singletons, 2491 discordant, 1053354 orphans, 8488 too large [>5000 bp], 7213795 duplicates)
Reads: 34640713 total, 36725 skipped (flags/unmapped)
Fragments: 17832253 total (16756458 tlen-paired, 2424 hash-paired, 306 singletons, 2107 discordant, 1070958 orphans, 5373 too large [>5000 bp], 7064132 duplicates)
Reads: 41597472 total, 75453 skipped (flags/unmapped)
Fragments: 21969121 total (18088780 tlen-paired, 1927 hash-paired, 317 singletons, 801013 discordant, 3077084 orphans, 330589 too large [>5000 bp], 8297634 duplicates)