Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/1c68b115c3db929beceec10d9f3ac7/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/d6da216ec4ddd2a8f2faf1d56a81f8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/1c68b115c3db929beceec10d9f3ac7/HCC1395_tumor.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/e8/d6da216ec4ddd2a8f2faf1d56a81f8/.command.run
==> 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: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Reads: 1116 total, 71 skipped (flags/unmapped)
Fragments: 542 total (503 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 39 orphans, 0 too large [>5000 bp], 7 duplicates)
Reads: 1706 total, 127 skipped (flags/unmapped)
Fragments: 799 total (779 tlen-paired, 0 hash-paired, 0 singletons, 1 discordant, 19 orphans, 0 too large [>5000 bp], 18 duplicates)
Reads: 1887 total, 242 skipped (flags/unmapped)
Fragments: 836 total (805 tlen-paired, 3 hash-paired, 0 singletons, 1 discordant, 27 orphans, 0 too large [>5000 bp], 24 duplicates)
Reads: 982842 total, 580 skipped (flags/unmapped)
Fragments: 491056 total (490674 tlen-paired, 180 hash-paired, 4 singletons, 26 discordant, 172 orphans, 163 too large [>5000 bp], 84350 duplicates)