Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_G9D-N1-BDNA-1_B23L5TMLT4_1/1029_G9D-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/bed11a0717f6b555e2ed3ccfd2ae3a/.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/df/bed11a0717f6b555e2ed3ccfd2ae3a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_G9D-N1-BDNA-1_B23L5TMLT4_1/1029_G9D-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: 1029_G9D-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G9D-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G9D-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G9D-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: 61521195 total, 50530 skipped (flags/unmapped)
Fragments: 30883298 total (30557313 tlen-paired, 3104 hash-paired, 386 singletons, 12140 discordant, 310355 orphans, 7405 too large [>5000 bp], 10715331 duplicates)
Reads: 65517446 total, 46154 skipped (flags/unmapped)
Fragments: 32891299 total (32532632 tlen-paired, 3440 hash-paired, 345 singletons, 10965 discordant, 343917 orphans, 16478 too large [>5000 bp], 11457300 duplicates)
Reads: 66662482 total, 42072 skipped (flags/unmapped)
Fragments: 33465096 total (33127121 tlen-paired, 3212 hash-paired, 411 singletons, 8535 discordant, 325817 orphans, 8223 too large [>5000 bp], 11408953 duplicates)
Reads: 72486608 total, 83924 skipped (flags/unmapped)
Fragments: 36512923 total (35530261 tlen-paired, 2787 hash-paired, 358 singletons, 194437 discordant, 785080 orphans, 81138 too large [>5000 bp], 12648084 duplicates)