Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/659_bPW-N1-BDNA-1_A23FG3YLT4_1/659_bPW-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/581e618e27f1d22b490579db97cabc/.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/b6/581e618e27f1d22b490579db97cabc/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/659_bPW-N1-BDNA-1_A23FG3YLT4_1/659_bPW-N1-BDNA-1_A23FG3YLT4_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_bPW-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bPW-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bPW-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bPW-N1-BDNA-1_A23FG3YLT4_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: 73910858 total, 55337 skipped (flags/unmapped)
Fragments: 37043610 total (36785221 tlen-paired, 3802 hash-paired, 359 singletons, 11212 discordant, 243016 orphans, 5838 too large [>5000 bp], 9349180 duplicates)
Reads: 81030607 total, 47489 skipped (flags/unmapped)
Fragments: 40613566 total (40340459 tlen-paired, 2940 hash-paired, 409 singletons, 8027 discordant, 261731 orphans, 9063 too large [>5000 bp], 10083130 duplicates)
Reads: 81425014 total, 53896 skipped (flags/unmapped)
Fragments: 40808879 total (40514281 tlen-paired, 4717 hash-paired, 346 singletons, 10415 discordant, 279120 orphans, 16413 too large [>5000 bp], 10205066 duplicates)
Reads: 82866858 total, 77831 skipped (flags/unmapped)
Fragments: 41635863 total (40894957 tlen-paired, 3480 hash-paired, 366 singletons, 139223 discordant, 597837 orphans, 57752 too large [>5000 bp], 10414426 duplicates)