Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_7OO-N1-BDNA-1_A237CFYLT3_1/1136_7OO-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/3fef3d8a5ff69a91e9774b5c2a15a6/.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/c3/3fef3d8a5ff69a91e9774b5c2a15a6/.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_7OO-N1-BDNA-1_A237CFYLT3_1/1136_7OO-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] [W::hts_idx_load3] The index file is older than the data file: 1136_7OO-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7OO-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_7OO-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7OO-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: 76501925 total, 80972 skipped (flags/unmapped)
Fragments: 38503130 total (37892448 tlen-paired, 5287 hash-paired, 10464 singletons, 9398 discordant, 585533 orphans, 5345 too large [>5000 bp], 7515616 duplicates)
Reads: 76915951 total, 74518 skipped (flags/unmapped)
Fragments: 38716735 total (38075257 tlen-paired, 8580 hash-paired, 10516 singletons, 8519 discordant, 613863 orphans, 16171 too large [>5000 bp], 7516776 duplicates)
Reads: 84064525 total, 77429 skipped (flags/unmapped)
Fragments: 42316003 total (41634672 tlen-paired, 7525 hash-paired, 11341 singletons, 6726 discordant, 655739 orphans, 11085 too large [>5000 bp], 8201029 duplicates)
Reads: 87387207 total, 183663 skipped (flags/unmapped)
Fragments: 44289292 total (42136199 tlen-paired, 6980 hash-paired, 11776 singletons, 430517 discordant, 1703820 orphans, 170278 too large [>5000 bp], 8479833 duplicates)