Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_1I8-N1-BDNA-1_A237CFYLT3_1/1136_1I8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/176a507de553986c8ad48913bc7bd8/.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/62/176a507de553986c8ad48913bc7bd8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_1I8-N1-BDNA-1_A237CFYLT3_1/1136_1I8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_1I8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1I8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_1I8-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1I8-N1-BDNA-1_A237CFYLT3_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: 59467528 total, 66873 skipped (flags/unmapped)
Fragments: 30181221 total (29197846 tlen-paired, 4127 hash-paired, 9706 singletons, 7381 discordant, 962161 orphans, 5040 too large [>5000 bp], 5995856 duplicates)
Reads: 65039278 total, 63176 skipped (flags/unmapped)
Fragments: 33031899 total (31919255 tlen-paired, 3092 hash-paired, 10108 singletons, 5364 discordant, 1094080 orphans, 8246 too large [>5000 bp], 6509413 duplicates)
Reads: 65563360 total, 63446 skipped (flags/unmapped)
Fragments: 33288962 total (32172103 tlen-paired, 2904 hash-paired, 10265 singletons, 7891 discordant, 1095799 orphans, 14027 too large [>5000 bp], 6579852 duplicates)
Reads: 70597991 total, 145242 skipped (flags/unmapped)
Fragments: 36455262 total (32642620 tlen-paired, 4608 hash-paired, 10730 singletons, 760649 discordant, 3036655 orphans, 294805 too large [>5000 bp], 6985951 duplicates)