Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_K08-N1-BDNA-1_B2377KTLT3_2/869_K08-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_K08-N1-BDNA-1_B2377KTLT3_2/869_K08-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/5f9edf3621830b6d8bf61ef8394bdc/.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/3a/5f9edf3621830b6d8bf61ef8394bdc/.command.run
==> 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_K08-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_K08-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_K08-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_K08-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: 89790428 total, 78820 skipped (flags/unmapped)
Fragments: 45093532 total (44573622 tlen-paired, 18381 hash-paired, 7028 singletons, 8033 discordant, 486468 orphans, 9020 too large [>5000 bp], 10750083 duplicates)
Reads: 97738845 total, 66600 skipped (flags/unmapped)
Fragments: 49109960 total (48518768 tlen-paired, 19123 hash-paired, 7614 singletons, 6124 discordant, 558331 orphans, 9135 too large [>5000 bp], 11738312 duplicates)
Reads: 99154386 total, 70213 skipped (flags/unmapped)
Fragments: 49809497 total (49218618 tlen-paired, 19105 hash-paired, 7773 singletons, 8191 discordant, 555810 orphans, 14381 too large [>5000 bp], 11817409 duplicates)
Reads: 102166825 total, 123955 skipped (flags/unmapped)
Fragments: 51618169 total (49758069 tlen-paired, 20404 hash-paired, 7980 singletons, 363798 discordant, 1467918 orphans, 141215 too large [>5000 bp], 12090197 duplicates)