Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/575169517271f75ca3dc73cb1e6646/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_annot.gtf
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/a04e6b1a84269c72052322ee552dca/aih-tih-sc-5ef3cb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/575169517271f75ca3dc73cb1e6646/.command.run
==> STAGING COMPLETE (8 inputs)

[2026-06-08T09:31:01] Launching Arriba 2.4.0
[2026-06-08T09:31:01] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:31:15] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:31:19] Reading chimeric alignments from 'aih-tih-sc-5ef3cb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' WARNING: (total=13664905)
169729 SAM records were malformed and ignored
[2026-06-08T09:38:39] Marking multi-mapping alignments (marked=9579844)
[2026-06-08T09:38:44] Detecting strandedness (reverse)
[2026-06-08T09:38:44] Assigning strands to alignments 
[2026-06-08T09:38:46] Annotating alignments 
[2026-06-08T09:39:23] Filtering duplicates (remaining=4764239)
[2026-06-08T09:39:29] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=4343711)
[2026-06-08T09:39:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4343711)
[2026-06-08T09:39:33] Filtering viral contigs with expression lower than the top 5 (remaining=4343711)
[2026-06-08T09:39:38] Filtering viral contigs with less than 5% coverage (remaining=4343711)
[2026-06-08T09:39:40] Estimating fragment length (mate gap mean=-84.0182, mate gap stddev=30.2844, read length mean=127.412)
[2026-06-08T09:39:40] Filtering read-through fragments with a distance <=10000bp (remaining=4218609)
[2026-06-08T09:39:43] Filtering inconsistently clipped mates (remaining=4141984)
[2026-06-08T09:39:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3941389)
[2026-06-08T09:39:48] Filtering fragments with small insert size (remaining=3940484)
[2026-06-08T09:39:50] Filtering alignments with long gaps (remaining=3940483)
[2026-06-08T09:39:52] Filtering fragments with both mates in the same gene (remaining=3939630)
[2026-06-08T09:39:54] Filtering fusions arising from hairpin structures (remaining=3759703)
[2026-06-08T09:39:57] Filtering reads with a mismatch p-value <=0.01 (remaining=1534056)
[2026-06-08T09:40:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=381954)
[2026-06-08T09:40:14] Finding fusions and counting supporting reads (total=WARNING: some fusions were subsampled, because they have more than 300 supporting reads
309057)
[2026-06-08T09:40:28] Merging adjacent fusion breakpoints (remaining=306676)
[2026-06-08T09:40:29] Filtering multi-mapping fusions by alignment score and read support (remaining=159593)
[2026-06-08T09:41:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:41:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=158258)
[2026-06-08T09:41:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=100504)
[2026-06-08T09:41:08] Filtering fusions with <2 supporting reads (remaining=8113)
[2026-06-08T09:41:08] Filtering fusions with an e-value >=0.3 (remaining=2460)
[2026-06-08T09:41:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2510)
[2026-06-08T09:41:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2367)
[2026-06-08T09:41:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2367)
[2026-06-08T09:41:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2199)
[2026-06-08T09:41:18] Searching for fusions with spliced split reads (remaining=2290)
[2026-06-08T09:41:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=1618)
[2026-06-08T09:41:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1590)
[2026-06-08T09:41:24] Searching for fusions with >=4 spliced events (remaining=1791)
[2026-06-08T09:41:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz'