Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_7BW-N1-BDNA-1_A237CFYLT3_1/1136_7BW-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/077bd2875e3b3da7d333ad938b0ea6/.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/50/077bd2875e3b3da7d333ad938b0ea6/.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_7BW-N1-BDNA-1_A237CFYLT3_1/1136_7BW-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
==> 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: 1136_7BW-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7BW-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7BW-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7BW-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: 88517530 total, 90748 skipped (flags/unmapped)
Fragments: 44571065 total (43799458 tlen-paired, 8564 hash-paired, 13248 singletons, 11855 discordant, 737940 orphans, 17920 too large [>5000 bp], 9402601 duplicates)
Reads: 88237080 total, 97883 skipped (flags/unmapped)
Fragments: 44424307 total (43680756 tlen-paired, 7295 hash-paired, 13775 singletons, 13507 discordant, 708974 orphans, 6666 too large [>5000 bp], 9400281 duplicates)
Reads: 96773080 total, 93600 skipped (flags/unmapped)
Fragments: 48730836 total (47904030 tlen-paired, 8449 hash-paired, 14507 singletons, 10149 discordant, 793701 orphans, 13008 too large [>5000 bp], 10262698 duplicates)
Reads: 100737320 total, 209957 skipped (flags/unmapped)
Fragments: 51083980 total (48517171 tlen-paired, 8258 hash-paired, 14884 singletons, 512180 discordant, 2031487 orphans, 202887 too large [>5000 bp], 10624244 duplicates)