Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/aa32ca09ff791d7a88376fcd79eef1/.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/62/aa32ca09ff791d7a88376fcd79eef1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BIHO-N1-BDNA-1_2375WFLT3_s34/1029_BIHO-N1-BDNA-1_2375WFLT3_s34.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BIHO-N1-BDNA-1_2375WFLT3_s34/1029_BIHO-N1-BDNA-1_2375WFLT3_s34.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BIHO-N1-BDNA-1_2375WFLT3_s34.recalibrated.bam.baiThe index file is older than the data file: 1029_BIHO-N1-BDNA-1_2375WFLT3_s34.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BIHO-N1-BDNA-1_2375WFLT3_s34.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BIHO-N1-BDNA-1_2375WFLT3_s34.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: 82256850 total, 66180 skipped (flags/unmapped)
Fragments: 41343002 total (40797075 tlen-paired, 3229 hash-paired, 1342 singletons, 12338 discordant, 529018 orphans, 17513 too large [>5000 bp], 12957047 duplicates)
Reads: 82073602 total, 73433 skipped (flags/unmapped)
Fragments: 41248140 total (40719420 tlen-paired, 4531 hash-paired, 1416 singletons, 14868 discordant, 507905 orphans, 6605 too large [>5000 bp], 13063955 duplicates)
Reads: 92312397 total, 116720 skipped (flags/unmapped)
Fragments: 46647254 total (44937551 tlen-paired, 3608 hash-paired, 1493 singletons, 335966 discordant, 1368636 orphans, 135649 too large [>5000 bp], 14516690 duplicates)
Reads: 89607020 total, 64158 skipped (flags/unmapped)
Fragments: 45040472 total (44467126 tlen-paired, 3443 hash-paired, 1426 singletons, 10599 discordant, 557878 orphans, 10611 too large [>5000 bp], 13959338 duplicates)