Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/bc60c169693496dc2575b72b3a2731/.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/6d/bc60c169693496dc2575b72b3a2731/.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_DOI-N1-BDNA-1_A237CFYLT3_1/869_DOI-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/869_DOI-N1-BDNA-1_A237CFYLT3_1/869_DOI-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: 869_DOI-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DOI-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DOI-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DOI-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: 87136210 total, 97523 skipped (flags/unmapped)
Fragments: 43756678 total (43246348 tlen-paired, 13914 hash-paired, 16544 singletons, 10897 discordant, 468975 orphans, 5425 too large [>5000 bp], 9158270 duplicates)
Reads: 94644435 total, 88644 skipped (flags/unmapped)
Fragments: 47531903 total (46982487 tlen-paired, 14842 hash-paired, 17518 singletons, 7983 discordant, 509073 orphans, 9288 too large [>5000 bp], 9913878 duplicates)
Reads: 95877160 total, 95340 skipped (flags/unmapped)
Fragments: 48145607 total (47570783 tlen-paired, 15912 hash-paired, 17599 singletons, 11640 discordant, 529673 orphans, 18939 too large [>5000 bp], 9993313 duplicates)
Reads: 98915283 total, 214181 skipped (flags/unmapped)
Fragments: 49892020 total (48211674 tlen-paired, 16730 hash-paired, 18364 singletons, 321052 discordant, 1324200 orphans, 129813 too large [>5000 bp], 10289911 duplicates)