Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/76ab78d70871b85415b10c650b0b38/.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/c3/76ab78d70871b85415b10c650b0b38/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7LD-N1-BDNA-1_A23NMNVLT4_1/1136_7LD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7LD-N1-BDNA-1_A23NMNVLT4_1/1136_7LD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_7LD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7LD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_7LD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7LD-N1-BDNA-1_A23NMNVLT4_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: 86204099 total, 65534 skipped (flags/unmapped)
Fragments: 43216559 total (42886411 tlen-paired, 3676 hash-paired, 356 singletons, 14009 discordant, 312107 orphans, 8955 too large [>5000 bp], 11481508 duplicates)
Reads: 92321301 total, 57816 skipped (flags/unmapped)
Fragments: 46283556 total (45948087 tlen-paired, 3648 hash-paired, 440 singletons, 10028 discordant, 321353 orphans, 9083 too large [>5000 bp], 12154087 duplicates)
Reads: 102445186 total, 93983 skipped (flags/unmapped)
Fragments: 51490126 total (50514291 tlen-paired, 4381 hash-paired, 497 singletons, 188029 discordant, 782928 orphans, 77188 too large [>5000 bp], 13928561 duplicates)
Reads: 101525279 total, 63597 skipped (flags/unmapped)
Fragments: 50903204 total (50504982 tlen-paired, 5015 hash-paired, 386 singletons, 14151 discordant, 378670 orphans, 17165 too large [>5000 bp], 13781542 duplicates)