Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_7L-N1-BDNA-1_A23H3NYLT3_1/1136_7L-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/81422fd6322ac958783130caa4e245/.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/67/81422fd6322ac958783130caa4e245/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_7L-N1-BDNA-1_A23H3NYLT3_1/1136_7L-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_7L-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7L-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_7L-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7L-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: 69543415 total, 53991 skipped (flags/unmapped)
Fragments: 34915800 total (34523992 tlen-paired, 20175 hash-paired, 8178 singletons, 6317 discordant, 357138 orphans, 11570 too large [>5000 bp], 4813819 duplicates)
Reads: 70150280 total, 62172 skipped (flags/unmapped)
Fragments: 35208845 total (34830759 tlen-paired, 21169 hash-paired, 8145 singletons, 7133 discordant, 341639 orphans, 10101 too large [>5000 bp], 4883156 duplicates)
Reads: 77714553 total, 57199 skipped (flags/unmapped)
Fragments: 39019777 total (38585531 tlen-paired, 22245 hash-paired, 8784 singletons, 5775 discordant, 397442 orphans, 12013 too large [>5000 bp], 5326035 duplicates)
Reads: 76988721 total, 89572 skipped (flags/unmapped)
Fragments: 38848144 total (37602886 tlen-paired, 20248 hash-paired, 8723 singletons, 242617 discordant, 973670 orphans, 92627 too large [>5000 bp], 5293353 duplicates)