Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/d1b526a8177f02d3db7b5ac3d7ece5/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_2E7-N1-BDNA-1_A23H3NYLT3_1/1136_2E7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_2E7-N1-BDNA-1_A23H3NYLT3_1/1136_2E7-N1-BDNA-1_A23H3NYLT3_1.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/91/d1b526a8177f02d3db7b5ac3d7ece5/.command.run
==> 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_2E7-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_2E7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2E7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2E7-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 36099832 total, 29594 skipped (flags/unmapped)
Fragments: 18106142 total (17941894 tlen-paired, 9581 hash-paired, 3010 singletons, 3427 discordant, 148230 orphans, 4597 too large [>5000 bp], 1860051 duplicates)
Reads: 38875091 total, 28220 skipped (flags/unmapped)
Fragments: 19502818 total (19316941 tlen-paired, 10886 hash-paired, 3433 singletons, 3458 discordant, 168100 orphans, 6384 too large [>5000 bp], 1983593 duplicates)
Reads: 39150777 total, 27905 skipped (flags/unmapped)
Fragments: 19642488 total (19456431 tlen-paired, 10047 hash-paired, 3267 singletons, 2980 discordant, 169763 orphans, 5463 too large [>5000 bp], 1994799 duplicates)
Reads: 39319949 total, 47883 skipped (flags/unmapped)
Fragments: 19808381 total (19274315 tlen-paired, 9737 hash-paired, 3301 singletons, 101833 discordant, 419195 orphans, 38900 too large [>5000 bp], 1997979 duplicates)