Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/6479d2b17561bfa38227313e3727f0/.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/cb/6479d2b17561bfa38227313e3727f0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_cwR-N1-BDNA-1_B23L5TMLT4_1/659_cwR-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_cwR-N1-BDNA-1_B23L5TMLT4_1/659_cwR-N1-BDNA-1_B23L5TMLT4_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_cwR-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cwR-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cwR-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cwR-N1-BDNA-1_B23L5TMLT4_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: 62367434 total, 48838 skipped (flags/unmapped)
Fragments: 31270242 total (31019217 tlen-paired, 4363 hash-paired, 340 singletons, 11448 discordant, 234874 orphans, 6663 too large [>5000 bp], 10481230 duplicates)
Reads: 66697811 total, 43031 skipped (flags/unmapped)
Fragments: 33439174 total (33188617 tlen-paired, 3247 hash-paired, 345 singletons, 7658 discordant, 239307 orphans, 8042 too large [>5000 bp], 11009129 duplicates)
Reads: 66080565 total, 44938 skipped (flags/unmapped)
Fragments: 33134407 total (32860040 tlen-paired, 3970 hash-paired, 331 singletons, 9992 discordant, 260074 orphans, 13609 too large [>5000 bp], 11165166 duplicates)
Reads: 72960750 total, 74650 skipped (flags/unmapped)
Fragments: 36662929 total (35969139 tlen-paired, 3053 hash-paired, 323 singletons, 135057 discordant, 555357 orphans, 57961 too large [>5000 bp], 12349622 duplicates)