Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/aefcfde861cc3d063436212406547e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/aefcfde861cc3d063436212406547e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/bed/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_chr21.bed
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam
==> 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: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Reads: 19949 total, 2364 skipped (flags/unmapped)
Fragments: 9048 total (8512 tlen-paired, 1 hash-paired, 0 singletons, 12 discordant, 523 orphans, 6 too large [>5000 bp], 412 duplicates)
Reads: 25740 total, 3806 skipped (flags/unmapped)
Fragments: 11208 total (10709 tlen-paired, 1 hash-paired, 1 singletons, 8 discordant, 489 orphans, 4 too large [>5000 bp], 567 duplicates)
Reads: 29685 total, 3160 skipped (flags/unmapped)
Fragments: 13528 total (12961 tlen-paired, 3 hash-paired, 0 singletons, 17 discordant, 547 orphans, 8 too large [>5000 bp], 810 duplicates)
Reads: 12123332 total, 7221 skipped (flags/unmapped)
Fragments: 6057287 total (6052480 tlen-paired, 2534 hash-paired, 63 singletons, 356 discordant, 1854 orphans, 1727 too large [>5000 bp], 1936089 duplicates)