Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/cdbe1c74b37045d732655932495918/.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/23/cdbe1c74b37045d732655932495918/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_MMQ-N1-BDNA-1_A23FG3YLT4_1/869_MMQ-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_MMQ-N1-BDNA-1_A23FG3YLT4_1/869_MMQ-N1-BDNA-1_A23FG3YLT4_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] The index file is older than the data file: 869_MMQ-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
The index file is older than the data file: 869_MMQ-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_MMQ-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_MMQ-N1-BDNA-1_A23FG3YLT4_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: 60990157 total, 38700 skipped (flags/unmapped)
Fragments: 30575956 total (30346734 tlen-paired, 2965 hash-paired, 290 singletons, 8190 discordant, 217777 orphans, 8806 too large [>5000 bp], 7015661 duplicates)
Reads: 60620114 total, 40794 skipped (flags/unmapped)
Fragments: 30391575 total (30164830 tlen-paired, 2946 hash-paired, 335 singletons, 10481 discordant, 212983 orphans, 4744 too large [>5000 bp], 7047188 duplicates)
Reads: 67227864 total, 37789 skipped (flags/unmapped)
Fragments: 33703870 total (33457822 tlen-paired, 3965 hash-paired, 316 singletons, 7574 discordant, 234193 orphans, 8422 too large [>5000 bp], 7632999 duplicates)
Reads: 67555866 total, 58935 skipped (flags/unmapped)
Fragments: 33956080 total (33321776 tlen-paired, 2002 hash-paired, 327 singletons, 121335 discordant, 510640 orphans, 47869 too large [>5000 bp], 7800387 duplicates)