Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/fb6174aa43430e705ca27358ed779d/.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/ca/fb6174aa43430e705ca27358ed779d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_TWH-N1-BDNA-1_B2377KTLT3_1/869_TWH-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_TWH-N1-BDNA-1_B2377KTLT3_1/869_TWH-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
==> 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: 869_TWH-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_TWH-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_TWH-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_TWH-N1-BDNA-1_B2377KTLT3_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: 78140272 total, 61821 skipped (flags/unmapped)
Fragments: 39261593 total (38786369 tlen-paired, 15000 hash-paired, 6709 singletons, 7109 discordant, 446406 orphans, 4190 too large [>5000 bp], 7936936 duplicates)
Reads: 79291313 total, 58579 skipped (flags/unmapped)
Fragments: 39842649 total (39345110 tlen-paired, 15018 hash-paired, 6474 singletons, 6245 discordant, 469802 orphans, 11856 too large [>5000 bp], 8027889 duplicates)
Reads: 86711875 total, 61899 skipped (flags/unmapped)
Fragments: 43580186 total (43027922 tlen-paired, 17553 hash-paired, 7244 singletons, 5353 discordant, 522114 orphans, 9481 too large [>5000 bp], 8807864 duplicates)
Reads: 89219417 total, 106698 skipped (flags/unmapped)
Fragments: 45093034 total (43403065 tlen-paired, 16041 hash-paired, 7368 singletons, 339681 discordant, 1326879 orphans, 130449 too large [>5000 bp], 8998703 duplicates)