Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/27bde2a35913869eb073dd9d3e736c/.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/b5/27bde2a35913869eb073dd9d3e736c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_exZ-N1-BDNA-1_A23TNVNLT4_1/659_exZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_exZ-N1-BDNA-1_A23TNVNLT4_1/659_exZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_exZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_exZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_exZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_exZ-N1-BDNA-1_A23TNVNLT4_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: 88198892 total, 60930 skipped (flags/unmapped)
Fragments: 44248852 total (43851202 tlen-paired, 3820 hash-paired, 338 singletons, 16008 discordant, 377484 orphans, 9040 too large [>5000 bp], 15676858 duplicates)
Reads: 95389849 total, 53180 skipped (flags/unmapped)
Fragments: 47859277 total (47441393 tlen-paired, 2982 hash-paired, 445 singletons, 11171 discordant, 403286 orphans, 10923 too large [>5000 bp], 16592338 duplicates)
Reads: 95103866 total, 55203 skipped (flags/unmapped)
Fragments: 47718174 total (47280449 tlen-paired, 3922 hash-paired, 367 singletons, 13512 discordant, 419924 orphans, 16303 too large [>5000 bp], 17094393 duplicates)
Reads: 105949354 total, 94904 skipped (flags/unmapped)
Fragments: 53311694 total (52101552 tlen-paired, 2551 hash-paired, 416 singletons, 244051 discordant, 963124 orphans, 97301 too large [>5000 bp], 19052887 duplicates)