Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/01ebc8364ad742fbb9dfbee7de7d29/.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/b6/01ebc8364ad742fbb9dfbee7de7d29/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_2F2-N1-BDNA-1_A23H3NYLT3_1/1136_2F2-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_2F2-N1-BDNA-1_A23H3NYLT3_1/1136_2F2-N1-BDNA-1_A23H3NYLT3_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: 1136_2F2-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_2F2-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_2F2-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2F2-N1-BDNA-1_A23H3NYLT3_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: 76293056 total, 64710 skipped (flags/unmapped)
Fragments: 38311397 total (37873649 tlen-paired, 13891 hash-paired, 7433 singletons, 8575 discordant, 407849 orphans, 10417 too large [>5000 bp], 5442579 duplicates)
Reads: 82174562 total, 60776 skipped (flags/unmapped)
Fragments: 41276207 total (40783763 tlen-paired, 14741 hash-paired, 7732 singletons, 8719 discordant, 461252 orphans, 15178 too large [>5000 bp], 5814107 duplicates)
Reads: 82832114 total, 58431 skipped (flags/unmapped)
Fragments: 41613268 total (41119836 tlen-paired, 13827 hash-paired, 7836 singletons, 6672 discordant, 465097 orphans, 10040 too large [>5000 bp], 5837253 duplicates)
Reads: 83818535 total, 99613 skipped (flags/unmapped)
Fragments: 42344958 total (40849128 tlen-paired, 14478 hash-paired, 7938 singletons, 288586 discordant, 1184828 orphans, 110886 too large [>5000 bp], 5893313 duplicates)