Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/32a89f2973ac8efcc36a5251872d7d/.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_1VE-N1-BDNA-1_A237CFYLT3_1/1136_1VE-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  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/1c/32a89f2973ac8efcc36a5251872d7d/.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_1VE-N1-BDNA-1_A237CFYLT3_1/1136_1VE-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] The index file is older than the data file: 1136_1VE-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1VE-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1VE-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1VE-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: 115306157 total, 123101 skipped (flags/unmapped)
Fragments: 57946538 total (57187873 tlen-paired, 15528 hash-paired, 17342 singletons, 16289 discordant, 709506 orphans, 8414 too large [>5000 bp], 12594998 duplicates)
Reads: 127034369 total, 116832 skipped (flags/unmapped)
Fragments: 63845935 total (62992860 tlen-paired, 16766 hash-paired, 18596 singletons, 16800 discordant, 800913 orphans, 22588 too large [>5000 bp], 13844289 duplicates)
Reads: 124462251 total, 113562 skipped (flags/unmapped)
Fragments: 62555260 total (61739789 tlen-paired, 16755 hash-paired, 18451 singletons, 11617 discordant, 768648 orphans, 12634 too large [>5000 bp], 13640576 duplicates)
Reads: 130681355 total, 277799 skipped (flags/unmapped)
Fragments: 66021356 total (63481611 tlen-paired, 17208 hash-paired, 19642 singletons, 485911 discordant, 2016984 orphans, 198735 too large [>5000 bp], 14193440 duplicates)