Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/a6d548a3270de2a7296ac630e27b7a/.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/15/a6d548a3270de2a7296ac630e27b7a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_5Z-N1-BDNA-1_B2377KTLT3_2/869_5Z-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_5Z-N1-BDNA-1_B2377KTLT3_2/869_5Z-N1-BDNA-1_B2377KTLT3_2.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: 869_5Z-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_5Z-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_5Z-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_5Z-N1-BDNA-1_B2377KTLT3_2.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: 73792050 total, 63360 skipped (flags/unmapped)
Fragments: 37074230 total (36624311 tlen-paired, 11363 hash-paired, 5583 singletons, 6108 discordant, 426865 orphans, 6339 too large [>5000 bp], 7783598 duplicates)
Reads: 80951851 total, 59059 skipped (flags/unmapped)
Fragments: 40690230 total (40168328 tlen-paired, 11715 hash-paired, 5970 singletons, 5023 discordant, 499194 orphans, 8748 too large [>5000 bp], 8547833 duplicates)
Reads: 81589566 total, 59721 skipped (flags/unmapped)
Fragments: 41006624 total (40479242 tlen-paired, 12838 hash-paired, 6076 singletons, 6417 discordant, 502051 orphans, 12362 too large [>5000 bp], 8542961 duplicates)
Reads: 84049443 total, 103758 skipped (flags/unmapped)
Fragments: 42503997 total (40849441 tlen-paired, 13424 hash-paired, 6412 singletons, 323003 discordant, 1311717 orphans, 127910 too large [>5000 bp], 8752109 duplicates)