Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_6B4-N1-BDNA-1_B23L5TMLT4_1/1136_6B4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/cbe1e4b396e9c6f32b5308c9747060/.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/70/cbe1e4b396e9c6f32b5308c9747060/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_6B4-N1-BDNA-1_B23L5TMLT4_1/1136_6B4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6B4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6B4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6B4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6B4-N1-BDNA-1_B23L5TMLT4_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: 84565856 total, 53094 skipped (flags/unmapped)
Fragments: 42428158 total (42024049 tlen-paired, 6590 hash-paired, 382 singletons, 10727 discordant, 386410 orphans, 21619 too large [>5000 bp], 14063286 duplicates)
Reads: 80174812 total, 59145 skipped (flags/unmapped)
Fragments: 40220363 total (39855971 tlen-paired, 4245 hash-paired, 364 singletons, 12970 discordant, 346813 orphans, 11059 too large [>5000 bp], 13287804 duplicates)
Reads: 85889780 total, 50085 skipped (flags/unmapped)
Fragments: 43091219 total (42714258 tlen-paired, 3293 hash-paired, 494 singletons, 8987 discordant, 364187 orphans, 10969 too large [>5000 bp], 13977942 duplicates)
Reads: 93591871 total, 91332 skipped (flags/unmapped)
Fragments: 47104098 total (45981942 tlen-paired, 3168 hash-paired, 426 singletons, 222887 discordant, 895675 orphans, 94222 too large [>5000 bp], 15571624 duplicates)