Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_5Z-N1-BDNA-1_B2377KTLT3_1/869_5Z-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/2c713ec56285caff580206982777d5/.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/85/2c713ec56285caff580206982777d5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_5Z-N1-BDNA-1_B2377KTLT3_1/869_5Z-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] [W::hts_idx_load3] The index file is older than the data file: 869_5Z-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.baiThe index file is older than the data file: 869_5Z-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_5Z-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_5Z-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: 75695137 total, 60002 skipped (flags/unmapped)
Fragments: 37958503 total (37634780 tlen-paired, 27505 hash-paired, 5869 singletons, 6323 discordant, 284026 orphans, 4012 too large [>5000 bp], 6771494 duplicates)
Reads: 83004077 total, 57826 skipped (flags/unmapped)
Fragments: 41630544 total (41264764 tlen-paired, 28054 hash-paired, 6317 singletons, 4863 discordant, 326546 orphans, 9013 too large [>5000 bp], 7432634 duplicates)
Reads: 84038421 total, 60034 skipped (flags/unmapped)
Fragments: 42144757 total (41772792 tlen-paired, 30637 hash-paired, 6531 singletons, 6637 discordant, 328160 orphans, 11782 too large [>5000 bp], 7471464 duplicates)
Reads: 85560239 total, 107514 skipped (flags/unmapped)
Fragments: 43061043 total (41992948 tlen-paired, 30281 hash-paired, 6660 singletons, 201945 discordant, 829209 orphans, 83254 too large [>5000 bp], 7604763 duplicates)