Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_DFS-N1-BDNA-1_B2377KTLT3_1/869_DFS-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_DFS-N1-BDNA-1_B2377KTLT3_1/869_DFS-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/71884357c7efece8be583598c9d107/.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/32/71884357c7efece8be583598c9d107/.command.run
==> 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_DFS-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
The index file is older than the data file: 869_DFS-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DFS-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DFS-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: 73991927 total, 61868 skipped (flags/unmapped)
Fragments: 37142049 total (36749278 tlen-paired, 22893 hash-paired, 5781 singletons, 6835 discordant, 357262 orphans, 4502 too large [>5000 bp], 6748549 duplicates)
Reads: 74475688 total, 59248 skipped (flags/unmapped)
Fragments: 37386811 total (36969141 tlen-paired, 24340 hash-paired, 5648 singletons, 6358 discordant, 381324 orphans, 14895 too large [>5000 bp], 6779324 duplicates)
Reads: 81071697 total, 60560 skipped (flags/unmapped)
Fragments: 40704144 total (40260117 tlen-paired, 23930 hash-paired, 6079 singletons, 5600 discordant, 408418 orphans, 8673 too large [>5000 bp], 7398902 duplicates)
Reads: 83137131 total, 110103 skipped (flags/unmapped)
Fragments: 41927496 total (40612906 tlen-paired, 25239 hash-paired, 6473 singletons, 256461 discordant, 1026417 orphans, 102463 too large [>5000 bp], 7543291 duplicates)