Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/03362df0fb957b4f37340342a569dd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/278f819846ff96c6923bdd66ccea66/Sig_18_tissue.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/4c/03362df0fb957b4f37340342a569dd/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/278f819846ff96c6923bdd66ccea66/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 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
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
Reads: 1601 total, 213 skipped (flags/unmapped)
Fragments: 714 total (671 tlen-paired, 0 hash-paired, 0 singletons, 1 discordant, 42 orphans, 1 too large [>5000 bp], 5 duplicates)
Reads: 1971 total, 313 skipped (flags/unmapped)
Fragments: 850 total (804 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 46 orphans, 2 too large [>5000 bp], 10 duplicates)
Reads: 2322 total, 261 skipped (flags/unmapped)
Fragments: 1056 total (1004 tlen-paired, 0 hash-paired, 0 singletons, 1 discordant, 51 orphans, 0 too large [>5000 bp], 14 duplicates)
Reads: 985372 total, 613 skipped (flags/unmapped)
Fragments: 492319 total (491974 tlen-paired, 168 hash-paired, 4 singletons, 22 discordant, 151 orphans, 138 too large [>5000 bp], 42102 duplicates)