Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_IE-N1-BDNA-1_A23NMNVLT4_1/1029_IE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_IE-N1-BDNA-1_A23NMNVLT4_1/1029_IE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/d38f5807548d31da02183d0795e724/.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/4b/d38f5807548d31da02183d0795e724/.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_IE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IE-N1-BDNA-1_A23NMNVLT4_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: 81327169 total, 48566 skipped (flags/unmapped)
Fragments: 40742237 total (40508867 tlen-paired, 2233 hash-paired, 349 singletons, 7830 discordant, 222958 orphans, 8718 too large [>5000 bp], 12411461 duplicates)
Reads: 75388533 total, 60769 skipped (flags/unmapped)
Fragments: 37763808 total (37532227 tlen-paired, 4124 hash-paired, 325 singletons, 11019 discordant, 216113 orphans, 8293 too large [>5000 bp], 11721999 duplicates)
Reads: 81943836 total, 51668 skipped (flags/unmapped)
Fragments: 41057476 total (40789679 tlen-paired, 3008 hash-paired, 287 singletons, 9945 discordant, 254557 orphans, 16030 too large [>5000 bp], 12850172 duplicates)
Reads: 90221949 total, 85292 skipped (flags/unmapped)
Fragments: 45269899 total (44634322 tlen-paired, 1778 hash-paired, 409 singletons, 124980 discordant, 508410 orphans, 52839 too large [>5000 bp], 14201817 duplicates)