Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/815e9898dc8ad1d1d10af7da295e55/.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/25/815e9898dc8ad1d1d10af7da295e55/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_5XC-N1-BDNA-1_A23KFG7LT4_1/1136_5XC-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_5XC-N1-BDNA-1_A23KFG7LT4_1/1136_5XC-N1-BDNA-1_A23KFG7LT4_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_5XC-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5XC-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5XC-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5XC-N1-BDNA-1_A23KFG7LT4_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: 74095313 total, 49428 skipped (flags/unmapped)
Fragments: 37122275 total (36892703 tlen-paired, 2420 hash-paired, 400 singletons, 10783 discordant, 215969 orphans, 8852 too large [>5000 bp], 12955424 duplicates)
Reads: 79489703 total, 43718 skipped (flags/unmapped)
Fragments: 39827524 total (39589805 tlen-paired, 2924 hash-paired, 397 singletons, 7600 discordant, 226798 orphans, 9066 too large [>5000 bp], 13544229 duplicates)
Reads: 78682811 total, 44062 skipped (flags/unmapped)
Fragments: 39425666 total (39172521 tlen-paired, 5223 hash-paired, 288 singletons, 9035 discordant, 238599 orphans, 13152 too large [>5000 bp], 13798889 duplicates)
Reads: 86446409 total, 80960 skipped (flags/unmapped)
Fragments: 43387885 total (42744032 tlen-paired, 3544 hash-paired, 363 singletons, 125606 discordant, 514340 orphans, 52191 too large [>5000 bp], 15193076 duplicates)