Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/d31cd06cd9a82feef706fb1254dc0e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_5JZ-N1-BDNA-1_A237CFYLT3_1/1136_5JZ-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_5JZ-N1-BDNA-1_A237CFYLT3_1/1136_5JZ-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/3a/d31cd06cd9a82feef706fb1254dc0e/.command.run
==> STAGING COMPLETE (5 inputs)

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_5JZ-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_5JZ-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_5JZ-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5JZ-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: 98043579 total, 92258 skipped (flags/unmapped)
Fragments: 49273266 total (48616480 tlen-paired, 11913 hash-paired, 15180 singletons, 11146 discordant, 618547 orphans, 19258 too large [>5000 bp], 10392709 duplicates)
Reads: 88516222 total, 94449 skipped (flags/unmapped)
Fragments: 44483558 total (43904941 tlen-paired, 10765 hash-paired, 13848 singletons, 10573 discordant, 543431 orphans, 5968 too large [>5000 bp], 9444269 duplicates)
Reads: 96943579 total, 87254 skipped (flags/unmapped)
Fragments: 48726829 total (48090004 tlen-paired, 11171 hash-paired, 14830 singletons, 7751 discordant, 603073 orphans, 10285 too large [>5000 bp], 10301665 duplicates)
Reads: 100705478 total, 209727 skipped (flags/unmapped)
Fragments: 50895639 total (48893611 tlen-paired, 11446 hash-paired, 15351 singletons, 386181 discordant, 1589050 orphans, 154437 too large [>5000 bp], 10645322 duplicates)