Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/b2e1c6257d583faad25cd887da6f88/.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_3T4-N1-BDNA-1_A237CFYLT3_1/1136_3T4-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/eb/b2e1c6257d583faad25cd887da6f88/.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_3T4-N1-BDNA-1_A237CFYLT3_1/1136_3T4-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_3T4-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_3T4-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_3T4-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_3T4-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: 66898328 total, 71291 skipped (flags/unmapped)
Fragments: 33840454 total (32945892 tlen-paired, 5440 hash-paired, 8828 singletons, 8461 discordant, 871833 orphans, 13395 too large [>5000 bp], 7314824 duplicates)
Reads: 66097313 total, 74299 skipped (flags/unmapped)
Fragments: 33430559 total (32569175 tlen-paired, 4177 hash-paired, 9146 singletons, 9363 discordant, 838698 orphans, 4870 too large [>5000 bp], 7278457 duplicates)
Reads: 72764447 total, 68529 skipped (flags/unmapped)
Fragments: 36817573 total (35848087 tlen-paired, 4185 hash-paired, 9464 singletons, 6931 discordant, 948906 orphans, 9571 too large [>5000 bp], 7957381 duplicates)
Reads: 77537151 total, 155416 skipped (flags/unmapped)
Fragments: 39701745 total (36514343 tlen-paired, 4674 hash-paired, 9941 singletons, 649127 discordant, 2523660 orphans, 255923 too large [>5000 bp], 8413403 duplicates)