Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_77Q-N1-BDNA-1_A237CFYLT3_1/1136_77Q-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/1136_77Q-N1-BDNA-1_A237CFYLT3_1/1136_77Q-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/53bcb86615171c7922971e8a2aa9d3/.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/64/53bcb86615171c7922971e8a2aa9d3/.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: 1136_77Q-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_77Q-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_77Q-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_77Q-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: 65869024 total, 75955 skipped (flags/unmapped)
Fragments: 33262828 total (32508861 tlen-paired, 3798 hash-paired, 9971 singletons, 8312 discordant, 731886 orphans, 4635 too large [>5000 bp], 6784377 duplicates)
Reads: 71991712 total, 70122 skipped (flags/unmapped)
Fragments: 36372212 total (35523081 tlen-paired, 3909 hash-paired, 10720 singletons, 6058 discordant, 828444 orphans, 8165 too large [>5000 bp], 7358269 duplicates)
Reads: 72850403 total, 72691 skipped (flags/unmapped)
Fragments: 36800058 total (35935109 tlen-paired, 4435 hash-paired, 10963 singletons, 8608 discordant, 840943 orphans, 14751 too large [>5000 bp], 7471088 duplicates)
Reads: 76830610 total, 173711 skipped (flags/unmapped)
Fragments: 39245945 total (36402016 tlen-paired, 4507 hash-paired, 11406 singletons, 565767 discordant, 2262249 orphans, 219332 too large [>5000 bp], 7770548 duplicates)