Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_7OO-N1-BDNA-1_A23H3NYLT3_1/1136_7OO-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/8242856678e28e77b90ba712957269/.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/5e/8242856678e28e77b90ba712957269/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_7OO-N1-BDNA-1_A23H3NYLT3_1/1136_7OO-N1-BDNA-1_A23H3NYLT3_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: 1136_7OO-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_7OO-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_7OO-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7OO-N1-BDNA-1_A23H3NYLT3_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: 83392314 total, 64723 skipped (flags/unmapped)
Fragments: 41912563 total (41360142 tlen-paired, 15888 hash-paired, 7600 singletons, 7378 discordant, 521555 orphans, 15810 too large [>5000 bp], 5790372 duplicates)
Reads: 84628001 total, 76626 skipped (flags/unmapped)
Fragments: 42514185 total (41994407 tlen-paired, 13651 hash-paired, 7938 singletons, 7804 discordant, 490385 orphans, 10664 too large [>5000 bp], 5918870 duplicates)
Reads: 92607928 total, 67907 skipped (flags/unmapped)
Fragments: 46547942 total (45941038 tlen-paired, 16626 hash-paired, 8291 singletons, 6487 discordant, 575500 orphans, 13964 too large [>5000 bp], 6387377 duplicates)
Reads: 92975026 total, 113954 skipped (flags/unmapped)
Fragments: 47020277 total (45190778 tlen-paired, 14314 hash-paired, 8426 singletons, 364589 discordant, 1442170 orphans, 135557 too large [>5000 bp], 6384646 duplicates)