Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_6F7-N1-BDNA-1_A23H3NYLT3_1/1136_6F7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/a8fe5b953d4959d735a2c22be8625a/.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/48/a8fe5b953d4959d735a2c22be8625a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_6F7-N1-BDNA-1_A23H3NYLT3_1/1136_6F7-N1-BDNA-1_A23H3NYLT3_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_6F7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6F7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6F7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6F7-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: 85977395 total, 69685 skipped (flags/unmapped)
Fragments: 43168683 total (42681375 tlen-paired, 14856 hash-paired, 9532 singletons, 7950 discordant, 454970 orphans, 17423 too large [>5000 bp], 5982544 duplicates)
Reads: 86809845 total, 74586 skipped (flags/unmapped)
Fragments: 43576573 total (43114423 tlen-paired, 15070 hash-paired, 9857 singletons, 8589 discordant, 428634 orphans, 10302 too large [>5000 bp], 6083423 duplicates)
Reads: 95039393 total, 69036 skipped (flags/unmapped)
Fragments: 47729497 total (47193474 tlen-paired, 17229 hash-paired, 10687 singletons, 6957 discordant, 501150 orphans, 11600 too large [>5000 bp], 6563608 duplicates)
Reads: 95103431 total, 118921 skipped (flags/unmapped)
Fragments: 47994604 total (46431851 tlen-paired, 15461 hash-paired, 10480 singletons, 307880 discordant, 1228932 orphans, 117357 too large [>5000 bp], 6568164 duplicates)