Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/e371f7b2079035c5704802e42707f5/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_VH9-N1-BDNA-1_B2377KTLT3_2/869_VH9-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam
  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/0c/e371f7b2079035c5704802e42707f5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_VH9-N1-BDNA-1_B2377KTLT3_2/869_VH9-N1-BDNA-1_B2377KTLT3_2.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: 869_VH9-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VH9-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VH9-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VH9-N1-BDNA-1_B2377KTLT3_2.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: 89122331 total, 78198 skipped (flags/unmapped)
Fragments: 44693533 total (44290759 tlen-paired, 29836 hash-paired, 7013 singletons, 8013 discordant, 357912 orphans, 10996 too large [>5000 bp], 9618717 duplicates)
Reads: 97282692 total, 70704 skipped (flags/unmapped)
Fragments: 48803951 total (48352336 tlen-paired, 30657 hash-paired, 7501 singletons, 6066 discordant, 407391 orphans, 9489 too large [>5000 bp], 10512169 duplicates)
Reads: 98174412 total, 71896 skipped (flags/unmapped)
Fragments: 49248613 total (48781387 tlen-paired, 32199 hash-paired, 7557 singletons, 8181 discordant, 419289 orphans, 16068 too large [>5000 bp], 10520759 duplicates)
Reads: 99961746 total, 129833 skipped (flags/unmapped)
Fragments: 50338866 total (49007893 tlen-paired, 34668 hash-paired, 7888 singletons, 250880 discordant, 1037537 orphans, 99803 too large [>5000 bp], 10705501 duplicates)