Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_4E9-N1-BDNA-1_A23H3NYLT3_1/1136_4E9-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/bef677b1d39335b751de4751a20215/.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/ae/bef677b1d39335b751de4751a20215/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_4E9-N1-BDNA-1_A23H3NYLT3_1/1136_4E9-N1-BDNA-1_A23H3NYLT3_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_4E9-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4E9-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4E9-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4E9-N1-BDNA-1_A23H3NYLT3_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: 72262245 total, 54884 skipped (flags/unmapped)
Fragments: 36330224 total (35832739 tlen-paired, 10670 hash-paired, 5225 singletons, 6990 discordant, 474600 orphans, 13369 too large [>5000 bp], 4950566 duplicates)
Reads: 73310981 total, 59222 skipped (flags/unmapped)
Fragments: 36846146 total (36368876 tlen-paired, 10245 hash-paired, 5426 singletons, 7206 discordant, 454393 orphans, 9643 too large [>5000 bp], 5053551 duplicates)
Reads: 80895710 total, 56397 skipped (flags/unmapped)
Fragments: 40679182 total (40123869 tlen-paired, 11186 hash-paired, 5880 singletons, 6360 discordant, 531887 orphans, 9358 too large [>5000 bp], 5515443 duplicates)
Reads: 80942825 total, 97890 skipped (flags/unmapped)
Fragments: 40962752 total (39281535 tlen-paired, 9823 hash-paired, 5883 singletons, 334307 discordant, 1331204 orphans, 128259 too large [>5000 bp], 5492186 duplicates)