Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_6K6-N1-BDNA-1_A23H3NYLT3_1/1136_6K6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/e95bf363b607465875c0187dc11a5f/.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/54/e95bf363b607465875c0187dc11a5f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_6K6-N1-BDNA-1_A23H3NYLT3_1/1136_6K6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6K6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6K6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6K6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6K6-N1-BDNA-1_A23H3NYLT3_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: 66453375 total, 52193 skipped (flags/unmapped)
Fragments: 33454963 total (32908171 tlen-paired, 8946 hash-paired, 6287 singletons, 6158 discordant, 525401 orphans, 11472 too large [>5000 bp], 4318598 duplicates)
Reads: 67183708 total, 63576 skipped (flags/unmapped)
Fragments: 33803418 total (33282029 tlen-paired, 7670 hash-paired, 6512 singletons, 6743 discordant, 500464 orphans, 10136 too large [>5000 bp], 4406484 duplicates)
Reads: 73253085 total, 50949 skipped (flags/unmapped)
Fragments: 36889496 total (36282220 tlen-paired, 6996 hash-paired, 6706 singletons, 5896 discordant, 587678 orphans, 8764 too large [>5000 bp], 4736716 duplicates)
Reads: 74569625 total, 91172 skipped (flags/unmapped)
Fragments: 37852794 total (35954723 tlen-paired, 7557 hash-paired, 7010 singletons, 384755 discordant, 1498749 orphans, 139312 too large [>5000 bp], 4780644 duplicates)