Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_GB9-N1-BDNA-1_B23L5TMLT4_1/1029_GB9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_GB9-N1-BDNA-1_B23L5TMLT4_1/1029_GB9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/6d4b5f550a4e424d8d6b4e459849e0/.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/50/6d4b5f550a4e424d8d6b4e459849e0/.command.run
==> 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_GB9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GB9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GB9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GB9-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: 94378879 total, 61146 skipped (flags/unmapped)
Fragments: 47395987 total (46858397 tlen-paired, 5366 hash-paired, 418 singletons, 16153 discordant, 515653 orphans, 20915 too large [>5000 bp], 17794956 duplicates)
Reads: 81620435 total, 62725 skipped (flags/unmapped)
Fragments: 40988848 total (40525130 tlen-paired, 3698 hash-paired, 451 singletons, 16332 discordant, 443237 orphans, 11851 too large [>5000 bp], 15391098 duplicates)
Reads: 86519539 total, 54396 skipped (flags/unmapped)
Fragments: 43451389 total (42973835 tlen-paired, 3593 hash-paired, 583 singletons, 11044 discordant, 462334 orphans, 12641 too large [>5000 bp], 15966871 duplicates)
Reads: 96175360 total, 94791 skipped (flags/unmapped)
Fragments: 48508402 total (47052306 tlen-paired, 2836 hash-paired, 499 singletons, 284131 discordant, 1168630 orphans, 116447 too large [>5000 bp], 18130087 duplicates)