Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BZM-N1-BDNA-1_B23L5TMLT4_1/1029_BZM-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_BZM-N1-BDNA-1_B23L5TMLT4_1/1029_BZM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/a1a48ee278f6b7368efafc3a92ab1f/.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/ee/a1a48ee278f6b7368efafc3a92ab1f/.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_BZM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BZM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BZM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BZM-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: 91374833 total, 56183 skipped (flags/unmapped)
Fragments: 45897614 total (45380494 tlen-paired, 4296 hash-paired, 575 singletons, 10676 discordant, 501573 orphans, 12785 too large [>5000 bp], 15969188 duplicates)
Reads: 85765184 total, 69401 skipped (flags/unmapped)
Fragments: 43073472 total (42578766 tlen-paired, 4531 hash-paired, 443 singletons, 15070 discordant, 474662 orphans, 11972 too large [>5000 bp], 15205230 duplicates)
Reads: 99236522 total, 59740 skipped (flags/unmapped)
Fragments: 49848225 total (49275897 tlen-paired, 4882 hash-paired, 483 singletons, 15350 discordant, 551613 orphans, 16214 too large [>5000 bp], 17679103 duplicates)
Reads: 100196925 total, 104317 skipped (flags/unmapped)
Fragments: 50560733 total (48961251 tlen-paired, 3533 hash-paired, 440 singletons, 310555 discordant, 1284954 orphans, 128268 too large [>5000 bp], 17838383 duplicates)