Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_38M-N1-BDNA-1_B23MHTGLT4_1/1029_38M-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/add203f743f7e4333ed7e5796abac0/.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/46/add203f743f7e4333ed7e5796abac0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_38M-N1-BDNA-1_B23MHTGLT4_1/1029_38M-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
==> 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: 1029_38M-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_38M-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_38M-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_38M-N1-BDNA-1_B23MHTGLT4_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: 100502925 total, 56097 skipped (flags/unmapped)
Fragments: 50506492 total (49908932 tlen-paired, 2715 hash-paired, 611 singletons, 7951 discordant, 586283 orphans, 10369 too large [>5000 bp], 17400465 duplicates)
Reads: 93503349 total, 69331 skipped (flags/unmapped)
Fragments: 46976218 total (46421230 tlen-paired, 4035 hash-paired, 524 singletons, 11145 discordant, 539284 orphans, 10695 too large [>5000 bp], 16675222 duplicates)
Reads: 98717367 total, 62331 skipped (flags/unmapped)
Fragments: 49604727 total (48981925 tlen-paired, 3490 hash-paired, 471 singletons, 9824 discordant, 609017 orphans, 27535 too large [>5000 bp], 17557910 duplicates)
Reads: 110134691 total, 101196 skipped (flags/unmapped)
Fragments: 55624434 total (53694581 tlen-paired, 3909 hash-paired, 543 singletons, 389973 discordant, 1535428 orphans, 160299 too large [>5000 bp], 19616195 duplicates)