Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_61R-N1-BDNA-1_B23L5TMLT4_1/1136_61R-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/2479bab2e5106778be302c29f5c257/.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/e5/2479bab2e5106778be302c29f5c257/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_61R-N1-BDNA-1_B23L5TMLT4_1/1136_61R-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_61R-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_61R-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_61R-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_61R-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: 77612462 total, 54087 skipped (flags/unmapped)
Fragments: 38936303 total (38581958 tlen-paired, 3975 hash-paired, 414 singletons, 12089 discordant, 337867 orphans, 12025 too large [>5000 bp], 14328344 duplicates)
Reads: 82050095 total, 49414 skipped (flags/unmapped)
Fragments: 41168747 total (40762013 tlen-paired, 3339 hash-paired, 423 singletons, 11746 discordant, 391226 orphans, 27418 too large [>5000 bp], 15166957 duplicates)
Reads: 90716146 total, 88368 skipped (flags/unmapped)
Fragments: 45658630 total (44571314 tlen-paired, 4129 hash-paired, 434 singletons, 214423 discordant, 868330 orphans, 89641 too large [>5000 bp], 16790098 duplicates)
Reads: 83302074 total, 46968 skipped (flags/unmapped)
Fragments: 41798160 total (41423837 tlen-paired, 3508 hash-paired, 453 singletons, 9299 discordant, 361063 orphans, 10151 too large [>5000 bp], 15080099 duplicates)