Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_0QH-N1-BDNA-1_A237CFYLT3_1/1136_0QH-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/bc7393e70feb4eb4807413b280bfb2/.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/b7/bc7393e70feb4eb4807413b280bfb2/.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_0QH-N1-BDNA-1_A237CFYLT3_1/1136_0QH-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
==> 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_0QH-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0QH-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0QH-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0QH-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: 51345177 total, 55457 skipped (flags/unmapped)
Fragments: 25904548 total (25368506 tlen-paired, 3273 hash-paired, 7298 singletons, 6437 discordant, 519034 orphans, 3478 too large [>5000 bp], 4393010 duplicates)
Reads: 55980369 total, 52722 skipped (flags/unmapped)
Fragments: 28253297 total (27654583 tlen-paired, 2851 hash-paired, 7700 singletons, 4624 discordant, 583539 orphans, 6146 too large [>5000 bp], 4770314 duplicates)
Reads: 56898005 total, 55230 skipped (flags/unmapped)
Fragments: 28710254 total (28103596 tlen-paired, 2875 hash-paired, 7923 singletons, 6716 discordant, 589144 orphans, 9667 too large [>5000 bp], 4835710 duplicates)
Reads: 59372106 total, 122462 skipped (flags/unmapped)
Fragments: 30269632 total (28275380 tlen-paired, 3064 hash-paired, 8073 singletons, 392416 discordant, 1590699 orphans, 154576 too large [>5000 bp], 5007471 duplicates)