Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/42bdc80b46a827786b0e9a0e72e188/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2E7-N1-BDNA-1_A237CFYLT3_1/1136_2E7-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  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/09/42bdc80b46a827786b0e9a0e72e188/.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_2E7-N1-BDNA-1_A237CFYLT3_1/1136_2E7-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_2E7-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_2E7-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2E7-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2E7-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: 34122092 total, 37145 skipped (flags/unmapped)
Fragments: 17135514 total (16934904 tlen-paired, 5330 hash-paired, 4823 singletons, 4389 discordant, 186068 orphans, 2405 too large [>5000 bp], 2601186 duplicates)
Reads: 37334464 total, 35359 skipped (flags/unmapped)
Fragments: 18749428 total (18531403 tlen-paired, 5252 hash-paired, 4860 singletons, 3262 discordant, 204651 orphans, 4880 too large [>5000 bp], 2833557 duplicates)
Reads: 37599822 total, 35725 skipped (flags/unmapped)
Fragments: 18882860 total (18656452 tlen-paired, 6431 hash-paired, 4969 singletons, 4468 discordant, 210540 orphans, 6943 too large [>5000 bp], 2844698 duplicates)
Reads: 38529187 total, 85179 skipped (flags/unmapped)
Fragments: 19436954 total (18771242 tlen-paired, 5662 hash-paired, 5036 singletons, 127554 discordant, 527460 orphans, 51298 too large [>5000 bp], 2907337 duplicates)