Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_8OI-N1-BDNA-1_235YY7LT3_1/1029_8OI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/e92019165c210983cf4f3e5b098acc/.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/b5/e92019165c210983cf4f3e5b098acc/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_8OI-N1-BDNA-1_235YY7LT3_1/1029_8OI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
==> 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: 1029_8OI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8OI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8OI-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8OI-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: 59682346 total, 51292 skipped (flags/unmapped)
Fragments: 29958187 total (29651747 tlen-paired, 2880 hash-paired, 3716 singletons, 9736 discordant, 290108 orphans, 4252 too large [>5000 bp], 6745609 duplicates)
Reads: 64419410 total, 46528 skipped (flags/unmapped)
Fragments: 32338274 total (32011430 tlen-paired, 2299 hash-paired, 3869 singletons, 7029 discordant, 313647 orphans, 6925 too large [>5000 bp], 7133210 duplicates)
Reads: 66709677 total, 75972 skipped (flags/unmapped)
Fragments: 33631506 total (32666231 tlen-paired, 3677 hash-paired, 4078 singletons, 182159 discordant, 775361 orphans, 75066 too large [>5000 bp], 7450283 duplicates)
Reads: 65908510 total, 51502 skipped (flags/unmapped)
Fragments: 33083217 total (32727589 tlen-paired, 6708 hash-paired, 3951 singletons, 10056 discordant, 334913 orphans, 14719 too large [>5000 bp], 7352987 duplicates)