Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/432cc3b06a5e43df919643262ee08a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_77B-N1-BDNA-1_B23KFG5LT4_1/1136_77B-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  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/09/432cc3b06a5e43df919643262ee08a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_77B-N1-BDNA-1_B23KFG5LT4_1/1136_77B-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_77B-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_77B-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_77B-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_77B-N1-BDNA-1_B23KFG5LT4_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: 72704170 total, 59277 skipped (flags/unmapped)
Fragments: 36468162 total (36136490 tlen-paired, 3352 hash-paired, 405 singletons, 15939 discordant, 311976 orphans, 10475 too large [>5000 bp], 15767350 duplicates)
Reads: 78040299 total, 49585 skipped (flags/unmapped)
Fragments: 39149469 total (38807030 tlen-paired, 2552 hash-paired, 497 singletons, 11275 discordant, 328115 orphans, 10194 too large [>5000 bp], 16442342 duplicates)
Reads: 78124424 total, 53043 skipped (flags/unmapped)
Fragments: 39189239 total (38825017 tlen-paired, 4678 hash-paired, 281 singletons, 13289 discordant, 345974 orphans, 19579 too large [>5000 bp], 16892167 duplicates)
Reads: 86111457 total, 84750 skipped (flags/unmapped)
Fragments: 43312224 total (42376939 tlen-paired, 4289 hash-paired, 384 singletons, 182675 discordant, 747937 orphans, 75290 too large [>5000 bp], 18682065 duplicates)