Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_8AV-N1-BDNA-1_235YY7LT3_1/1029_8AV-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_8AV-N1-BDNA-1_235YY7LT3_1/1029_8AV-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/4a1d317abff9e68436aa586a1dd37e/.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/7a/4a1d317abff9e68436aa586a1dd37e/.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: 1029_8AV-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8AV-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8AV-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_8AV-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: 77364569 total, 53938 skipped (flags/unmapped)
Fragments: 38822979 total (38456179 tlen-paired, 3852 hash-paired, 4303 singletons, 8613 discordant, 350032 orphans, 9504 too large [>5000 bp], 8795553 duplicates)
Reads: 71745962 total, 54296 skipped (flags/unmapped)
Fragments: 36002606 total (35659084 tlen-paired, 4345 hash-paired, 3942 singletons, 9485 discordant, 325750 orphans, 8073 too large [>5000 bp], 8220471 duplicates)
Reads: 71340267 total, 58776 skipped (flags/unmapped)
Fragments: 35800198 total (35454874 tlen-paired, 4284 hash-paired, 3947 singletons, 11411 discordant, 325682 orphans, 5362 too large [>5000 bp], 8264196 duplicates)
Reads: 79735155 total, 80448 skipped (flags/unmapped)
Fragments: 40165669 total (39116099 tlen-paired, 2235 hash-paired, 4556 singletons, 205308 discordant, 837471 orphans, 82698 too large [>5000 bp], 9137188 duplicates)