Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_OLD-N1-BDNA-1_B2377KTLT3_3/869_OLD-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_OLD-N1-BDNA-1_B2377KTLT3_3/869_OLD-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/7f7f958f5f9fe7be394cebc0189f23/.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/ea/7f7f958f5f9fe7be394cebc0189f23/.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: 869_OLD-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_OLD-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_OLD-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_OLD-N1-BDNA-1_B2377KTLT3_3.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: 92306568 total, 83564 skipped (flags/unmapped)
Fragments: 46281683 total (45868435 tlen-paired, 40078 hash-paired, 6351 singletons, 9000 discordant, 357819 orphans, 11904 too large [>5000 bp], 11055108 duplicates)
Reads: 100957490 total, 70980 skipped (flags/unmapped)
Fragments: 50634495 total (50181511 tlen-paired, 41082 hash-paired, 6689 singletons, 6598 discordant, 398615 orphans, 11412 too large [>5000 bp], 12123379 duplicates)
Reads: 100788048 total, 72812 skipped (flags/unmapped)
Fragments: 50553084 total (50075376 tlen-paired, 42340 hash-paired, 6714 singletons, 8898 discordant, 419756 orphans, 17769 too large [>5000 bp], 12021358 duplicates)
Reads: 104029533 total, 130453 skipped (flags/unmapped)
Fragments: 52359817 total (51053397 tlen-paired, 44628 hash-paired, 7146 singletons, 242916 discordant, 1011730 orphans, 99161 too large [>5000 bp], 12397959 duplicates)