Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_4DU-N1-BDNA-1_B23KFG5LT4_1/1136_4DU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_4DU-N1-BDNA-1_B23KFG5LT4_1/1136_4DU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/2b1444a61f7c9ae1fc4b4d5982f8c5/.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/2c/2b1444a61f7c9ae1fc4b4d5982f8c5/.command.run
==> 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_4DU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4DU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4DU-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4DU-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: 89576240 total, 66048 skipped (flags/unmapped)
Fragments: 44948560 total (44517869 tlen-paired, 3487 hash-paired, 441 singletons, 17426 discordant, 409337 orphans, 11425 too large [>5000 bp], 19867084 duplicates)
Reads: 95628465 total, 61092 skipped (flags/unmapped)
Fragments: 47991782 total (47497888 tlen-paired, 5800 hash-paired, 366 singletons, 15323 discordant, 472405 orphans, 28290 too large [>5000 bp], 21180909 duplicates)
Reads: 95249092 total, 60574 skipped (flags/unmapped)
Fragments: 47799156 total (47344875 tlen-paired, 3617 hash-paired, 444 singletons, 12798 discordant, 437422 orphans, 14036 too large [>5000 bp], 20628522 duplicates)
Reads: 107006361 total, 101450 skipped (flags/unmapped)
Fragments: 53861706 total (52573575 tlen-paired, 3876 hash-paired, 440 singletons, 257632 discordant, 1026183 orphans, 104061 too large [>5000 bp], 23694690 duplicates)