Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/3aba120cd7f8a4dd4c8844b641a37c/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_ef5-N1-BDNA-1_A23TY32LT4_1/659_ef5-N1-BDNA-1_A23TY32LT4_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/1a/3aba120cd7f8a4dd4c8844b641a37c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_ef5-N1-BDNA-1_A23TY32LT4_1/659_ef5-N1-BDNA-1_A23TY32LT4_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: 659_ef5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ef5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ef5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ef5-N1-BDNA-1_A23TY32LT4_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: 74311550 total, 60990 skipped (flags/unmapped)
Fragments: 37238695 total (36974939 tlen-paired, 4509 hash-paired, 341 singletons, 12277 discordant, 246629 orphans, 10070 too large [>5000 bp], 13385072 duplicates)
Reads: 88259056 total, 55556 skipped (flags/unmapped)
Fragments: 44232305 total (43918535 tlen-paired, 6257 hash-paired, 280 singletons, 12323 discordant, 294910 orphans, 17040 too large [>5000 bp], 16015355 duplicates)
Reads: 81845475 total, 51875 skipped (flags/unmapped)
Fragments: 41014140 total (40744200 tlen-paired, 4323 hash-paired, 448 singletons, 8381 discordant, 256788 orphans, 11278 too large [>5000 bp], 14522309 duplicates)
Reads: 88744926 total, 91853 skipped (flags/unmapped)
Fragments: 44570156 total (43818757 tlen-paired, 4932 hash-paired, 312 singletons, 143980 discordant, 602175 orphans, 57624 too large [>5000 bp], 16133508 duplicates)