Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_cAr-N1-BDNA-1_B23L5TMLT4_1/659_cAr-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/0159ebf2994c7b3b37ebc689dcfcec/.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/1d/0159ebf2994c7b3b37ebc689dcfcec/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_cAr-N1-BDNA-1_B23L5TMLT4_1/659_cAr-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: 659_cAr-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cAr-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cAr-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cAr-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: 78612140 total, 63336 skipped (flags/unmapped)
Fragments: 39424139 total (39085013 tlen-paired, 4455 hash-paired, 562 singletons, 15509 discordant, 318600 orphans, 9844 too large [>5000 bp], 14166188 duplicates)
Reads: 83373171 total, 56602 skipped (flags/unmapped)
Fragments: 41813071 total (41443278 tlen-paired, 6114 hash-paired, 433 singletons, 13316 discordant, 349930 orphans, 20395 too large [>5000 bp], 15095174 duplicates)
Reads: 84462615 total, 52931 skipped (flags/unmapped)
Fragments: 42359313 total (42011938 tlen-paired, 4297 hash-paired, 492 singletons, 10956 discordant, 331630 orphans, 11590 too large [>5000 bp], 14973767 duplicates)
Reads: 92223640 total, 99544 skipped (flags/unmapped)
Fragments: 46364756 total (45413285 tlen-paired, 4834 hash-paired, 474 singletons, 185391 discordant, 760772 orphans, 77915 too large [>5000 bp], 16674456 duplicates)