Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/f6212588a9e1ef904c0e986751c18f/.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/73/f6212588a9e1ef904c0e986751c18f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_Z5S-N1-BDNA-1_A23TY32LT4_1/1241_Z5S-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_Z5S-N1-BDNA-1_A23TY32LT4_1/1241_Z5S-N1-BDNA-1_A23TY32LT4_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: 1241_Z5S-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Z5S-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Z5S-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Z5S-N1-BDNA-1_A23TY32LT4_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: 95180388 total, 68880 skipped (flags/unmapped)
Fragments: 47746976 total (47330556 tlen-paired, 3181 hash-paired, 437 singletons, 13137 discordant, 399665 orphans, 8829 too large [>5000 bp], 20619925 duplicates)
Reads: 101903898 total, 63621 skipped (flags/unmapped)
Fragments: 51122371 total (50677552 tlen-paired, 4902 hash-paired, 499 singletons, 8956 discordant, 430462 orphans, 13248 too large [>5000 bp], 21761143 duplicates)
Reads: 112550353 total, 65349 skipped (flags/unmapped)
Fragments: 56468142 total (55958707 tlen-paired, 4401 hash-paired, 335 singletons, 13902 discordant, 490797 orphans, 19926 too large [>5000 bp], 24561051 duplicates)
Reads: 114136926 total, 111988 skipped (flags/unmapped)
Fragments: 57453294 total (56079870 tlen-paired, 2826 hash-paired, 398 singletons, 272282 discordant, 1097918 orphans, 108333 too large [>5000 bp], 24849314 duplicates)