Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/3efcbed21b1f0a0fefe175867f8393/.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/f2/3efcbed21b1f0a0fefe175867f8393/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_SP-N1-BDNA-1_B23KFG5LT4_1/659_SP-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_SP-N1-BDNA-1_B23KFG5LT4_1/659_SP-N1-BDNA-1_B23KFG5LT4_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: 659_SP-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_SP-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_SP-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_SP-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: 87571233 total, 68165 skipped (flags/unmapped)
Fragments: 43887793 total (43559849 tlen-paired, 3599 hash-paired, 422 singletons, 21363 discordant, 302560 orphans, 15232 too large [>5000 bp], 17078524 duplicates)
Reads: 92548312 total, 57394 skipped (flags/unmapped)
Fragments: 46383616 total (46065315 tlen-paired, 4282 hash-paired, 398 singletons, 14347 discordant, 299274 orphans, 11679 too large [>5000 bp], 17700672 duplicates)
Reads: 102706144 total, 97543 skipped (flags/unmapped)
Fragments: 51559561 total (50786176 tlen-paired, 3804 hash-paired, 386 singletons, 140986 discordant, 628209 orphans, 59037 too large [>5000 bp], 20235788 duplicates)
Reads: 102123328 total, 63451 skipped (flags/unmapped)
Fragments: 51186759 total (50790343 tlen-paired, 5212 hash-paired, 344 singletons, 21657 discordant, 369203 orphans, 27953 too large [>5000 bp], 20054116 duplicates)