Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/8a678ecbad45df2329e4305e19b158/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_75V-N1-BDNA-1_A237CFYLT3_1/1136_75V-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  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/28/8a678ecbad45df2329e4305e19b158/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_75V-N1-BDNA-1_A237CFYLT3_1/1136_75V-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
==> 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: 1136_75V-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_75V-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_75V-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_75V-N1-BDNA-1_A237CFYLT3_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: 80533031 total, 93136 skipped (flags/unmapped)
Fragments: 40660239 total (39747495 tlen-paired, 5546 hash-paired, 11757 singletons, 13991 discordant, 881450 orphans, 6312 too large [>5000 bp], 9845784 duplicates)
Reads: 81523449 total, 84070 skipped (flags/unmapped)
Fragments: 41165147 total (40235540 tlen-paired, 6844 hash-paired, 11851 singletons, 11370 discordant, 899542 orphans, 10239 too large [>5000 bp], 9970436 duplicates)
Reads: 88023426 total, 83878 skipped (flags/unmapped)
Fragments: 44458114 total (43446773 tlen-paired, 5462 hash-paired, 12393 singletons, 9755 discordant, 983731 orphans, 9722 too large [>5000 bp], 10745170 duplicates)
Reads: 93473106 total, 203661 skipped (flags/unmapped)
Fragments: 47672903 total (44414692 tlen-paired, 6904 hash-paired, 13033 singletons, 656566 discordant, 2581708 orphans, 259190 too large [>5000 bp], 11331346 duplicates)