Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1029_FSS-N1-BDNA-1_A237CFYLT3_1/1029_FSS-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1029_FSS-N1-BDNA-1_A237CFYLT3_1/1029_FSS-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/c3412b8e515ee35cb79ab36f0ca88f/.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/70/c3412b8e515ee35cb79ab36f0ca88f/.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: 1029_FSS-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FSS-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FSS-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FSS-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: 58292985 total, 66817 skipped (flags/unmapped)
Fragments: 29315203 total (28889219 tlen-paired, 6072 hash-paired, 9249 singletons, 7488 discordant, 403175 orphans, 4093 too large [>5000 bp], 5228096 duplicates)
Reads: 63431728 total, 63400 skipped (flags/unmapped)
Fragments: 31906524 total (31434130 tlen-paired, 7057 hash-paired, 9932 singletons, 5843 discordant, 449562 orphans, 7387 too large [>5000 bp], 5704898 duplicates)
Reads: 64722150 total, 62457 skipped (flags/unmapped)
Fragments: 32554474 total (32073298 tlen-paired, 8138 hash-paired, 10180 singletons, 7713 discordant, 455145 orphans, 8035 too large [>5000 bp], 5785126 duplicates)
Reads: 66396511 total, 146642 skipped (flags/unmapped)
Fragments: 33610243 total (32112210 tlen-paired, 6871 hash-paired, 10411 singletons, 289041 discordant, 1191710 orphans, 115752 too large [>5000 bp], 5906777 duplicates)