Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/16a6997424e6587b69acf44ce61e73/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_LSE-N1-BDNA-1_A237CFYLT3_1/869_LSE-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  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/cd/16a6997424e6587b69acf44ce61e73/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_LSE-N1-BDNA-1_A237CFYLT3_1/869_LSE-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: 869_LSE-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_LSE-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 869_LSE-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_LSE-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: 109634732 total, 122639 skipped (flags/unmapped)
Fragments: 55083905 total (54385520 tlen-paired, 14419 hash-paired, 18822 singletons, 13787 discordant, 651357 orphans, 7231 too large [>5000 bp], 14024152 duplicates)
Reads: 119481516 total, 111923 skipped (flags/unmapped)
Fragments: 60040702 total (59283092 tlen-paired, 14046 hash-paired, 19548 singletons, 9745 discordant, 714271 orphans, 11004 too large [>5000 bp], 15252015 duplicates)
Reads: 121383377 total, 117534 skipped (flags/unmapped)
Fragments: 60994015 total (60200247 tlen-paired, 14787 hash-paired, 20218 singletons, 14000 discordant, 744763 orphans, 21397 too large [>5000 bp], 15422007 duplicates)
Reads: 124981311 total, 281259 skipped (flags/unmapped)
Fragments: 63114877 total (60738013 tlen-paired, 16144 hash-paired, 20741 singletons, 458148 discordant, 1881831 orphans, 186435 too large [>5000 bp], 15837324 duplicates)