Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_FOO-N1-BDNA-1_235YY7LT3_1/1029_FOO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/7aa318e7eae3df8e3c102432e06d6b/.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/22/7aa318e7eae3df8e3c102432e06d6b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_FOO-N1-BDNA-1_235YY7LT3_1/1029_FOO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
==> 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: 1029_FOO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_FOO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FOO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FOO-N1-BDNA-1_235YY7LT3_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: 44283653 total, 43626 skipped (flags/unmapped)
Fragments: 22471069 total (21755261 tlen-paired, 2349 hash-paired, 2403 singletons, 4874 discordant, 706182 orphans, 3237 too large [>5000 bp], 5700935 duplicates)
Reads: 49187128 total, 44149 skipped (flags/unmapped)
Fragments: 24966138 total (24150742 tlen-paired, 4397 hash-paired, 2479 singletons, 5104 discordant, 803416 orphans, 8299 too large [>5000 bp], 6244488 duplicates)
Reads: 47817791 total, 42377 skipped (flags/unmapped)
Fragments: 24272706 total (23484411 tlen-paired, 2174 hash-paired, 2445 singletons, 3707 discordant, 779969 orphans, 6208 too large [>5000 bp], 6004527 duplicates)
Reads: 52097358 total, 73140 skipped (flags/unmapped)
Fragments: 26898811 total (24134864 tlen-paired, 2068 hash-paired, 2684 singletons, 546277 discordant, 2212918 orphans, 221099 too large [>5000 bp], 6401895 duplicates)