Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/5aff09d7fee5de4e4172b985bfcfce/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_EFW-N1-BDNA-1_235YY7LT3_1/1029_EFW-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  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/b9/5aff09d7fee5de4e4172b985bfcfce/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_EFW-N1-BDNA-1_235YY7LT3_1/1029_EFW-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] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_EFW-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.baiThe index file is older than the data file: 1029_EFW-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
The index file is older than the data file: 1029_EFW-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_EFW-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: 56963107 total, 47943 skipped (flags/unmapped)
Fragments: 28593821 total (28301428 tlen-paired, 2897 hash-paired, 3275 singletons, 8770 discordant, 277451 orphans, 4124 too large [>5000 bp], 6898170 duplicates)
Reads: 62766403 total, 48011 skipped (flags/unmapped)
Fragments: 31504546 total (31178020 tlen-paired, 3275 hash-paired, 3471 singletons, 8243 discordant, 311537 orphans, 12154 too large [>5000 bp], 7510968 duplicates)
Reads: 61374292 total, 44308 skipped (flags/unmapped)
Fragments: 30808130 total (30497610 tlen-paired, 2532 hash-paired, 3452 singletons, 6250 discordant, 298286 orphans, 7731 too large [>5000 bp], 7261053 duplicates)
Reads: 63687567 total, 69586 skipped (flags/unmapped)
Fragments: 32110497 total (31178136 tlen-paired, 2457 hash-paired, 3620 singletons, 177895 discordant, 748389 orphans, 74498 too large [>5000 bp], 7619065 duplicates)