Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_0L8-N1-BDNA-1_A237CFYLT3_1/1136_0L8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/45c0ce291737b41599c635fe0bea47/.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/df/45c0ce291737b41599c635fe0bea47/.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_0L8-N1-BDNA-1_A237CFYLT3_1/1136_0L8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_0L8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_0L8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0L8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0L8-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: 88740602 total, 81942 skipped (flags/unmapped)
Fragments: 44613264 total (43991004 tlen-paired, 7872 hash-paired, 11847 singletons, 9548 discordant, 592993 orphans, 18486 too large [>5000 bp], 8946782 duplicates)
Reads: 96619722 total, 81770 skipped (flags/unmapped)
Fragments: 48585623 total (47919210 tlen-paired, 7000 hash-paired, 12896 singletons, 7671 discordant, 638846 orphans, 9224 too large [>5000 bp], 9749362 duplicates)
Reads: 87824743 total, 86659 skipped (flags/unmapped)
Fragments: 44148576 total (43563500 tlen-paired, 5852 hash-paired, 11818 singletons, 9956 discordant, 557450 orphans, 5100 too large [>5000 bp], 8911264 duplicates)
Reads: 100510771 total, 199218 skipped (flags/unmapped)
Fragments: 50814287 total (48763022 tlen-paired, 6789 hash-paired, 13396 singletons, 410797 discordant, 1620283 orphans, 158329 too large [>5000 bp], 10086347 duplicates)