Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_5Z2-N1-BDNA-1_A237CFYLT3_1/1136_5Z2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/b2d6960c6d2ac95906d24c4c76d419/.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/39/b2d6960c6d2ac95906d24c4c76d419/.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_5Z2-N1-BDNA-1_A237CFYLT3_1/1136_5Z2-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_5Z2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5Z2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5Z2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5Z2-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: 94215863 total, 92433 skipped (flags/unmapped)
Fragments: 47329068 total (46738388 tlen-paired, 11360 hash-paired, 15363 singletons, 10568 discordant, 553389 orphans, 17023 too large [>5000 bp], 9679018 duplicates)
Reads: 93643356 total, 100085 skipped (flags/unmapped)
Fragments: 47040283 total (46467896 tlen-paired, 12237 hash-paired, 15665 singletons, 11451 discordant, 533034 orphans, 5702 too large [>5000 bp], 9662417 duplicates)
Reads: 103217546 total, 90944 skipped (flags/unmapped)
Fragments: 51856543 total (51227137 tlen-paired, 11619 hash-paired, 16753 singletons, 8469 discordant, 592565 orphans, 11417 too large [>5000 bp], 10613014 duplicates)
Reads: 106225608 total, 223579 skipped (flags/unmapped)
Fragments: 53608501 total (51700962 tlen-paired, 13517 hash-paired, 17493 singletons, 373183 discordant, 1503346 orphans, 152933 too large [>5000 bp], 10885102 duplicates)