Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/4b333830e6d52085795bc8fb6f0fff/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_LVG-N1-BDNA-1_B2377KTLT3_2/869_LVG-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
  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/83/4b333830e6d52085795bc8fb6f0fff/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_LVG-N1-BDNA-1_B2377KTLT3_2/869_LVG-N1-BDNA-1_B2377KTLT3_2.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: 869_LVG-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_LVG-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
The index file is older than the data file: 869_LVG-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_LVG-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: 103807211 total, 96557 skipped (flags/unmapped)
Fragments: 52060684 total (51575316 tlen-paired, 39510 hash-paired, 8723 singletons, 10944 discordant, 426191 orphans, 12100 too large [>5000 bp], 15187717 duplicates)
Reads: 113350307 total, 84288 skipped (flags/unmapped)
Fragments: 56862726 total (56325920 tlen-paired, 41280 hash-paired, 9333 singletons, 7943 discordant, 478250 orphans, 14075 too large [>5000 bp], 16530134 duplicates)
Reads: 114144166 total, 90034 skipped (flags/unmapped)
Fragments: 57255718 total (56699147 tlen-paired, 45841 hash-paired, 9309 singletons, 11010 discordant, 490411 orphans, 21208 too large [>5000 bp], 16616561 duplicates)
Reads: 117216334 total, 151213 skipped (flags/unmapped)
Fragments: 59024449 total (57470596 tlen-paired, 44160 hash-paired, 9892 singletons, 291564 discordant, 1208237 orphans, 117176 too large [>5000 bp], 17046169 duplicates)