Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/249a25a25cef4e7191b8fe603f4e81/.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/c9/249a25a25cef4e7191b8fe603f4e81/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/e04f013b5266d6b8acb979791f0560/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/e04f013b5266d6b8acb979791f0560/Sig_18_Blood.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_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
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: 1021 total, 85 skipped (flags/unmapped)
Fragments: 470 total (466 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 4 orphans, 0 too large [>5000 bp], 4 duplicates)
Reads: 1593 total, 135 skipped (flags/unmapped)
Fragments: 729 total (729 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 0 orphans, 0 too large [>5000 bp], 23 duplicates)
Reads: 1477 total, 263 skipped (flags/unmapped)
Fragments: 606 total (604 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 2 orphans, 2 too large [>5000 bp], 4 duplicates)
Reads: 985708 total, 312 skipped (flags/unmapped)
Fragments: 492568 total (492473 tlen-paired, 52 hash-paired, 7 singletons, 3 discordant, 33 orphans, 150 too large [>5000 bp], 57646 duplicates)