[2026-06-08T08:21:00] Launching Arriba 2.4.0
[2026-06-08T08:21:00] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:14] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:21:19] Reading chimeric alignments from 'aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=7059030)
[2026-06-08T08:26:01] Marking multi-mapping alignments (marked=4798453)
[2026-06-08T08:26:04] Detecting strandedness (reverse)
[2026-06-08T08:26:04] Assigning strands to alignments 
[2026-06-08T08:26:05] Annotating alignments 
[2026-06-08T08:26:27] Filtering duplicates (remaining=3086084)
[2026-06-08T08:26:31] 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=2875831)
[2026-06-08T08:26:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2875831)
[2026-06-08T08:26:34] Filtering viral contigs with expression lower than the top 5 (remaining=2875831)
[2026-06-08T08:26:36] Filtering viral contigs with less than 5% coverage (remaining=2875831)
[2026-06-08T08:26:38] Estimating fragment length (mate gap mean=-82.4629, mate gap stddev=27.7892, read length mean=119.692)
[2026-06-08T08:26:38] Filtering read-through fragments with a distance <=10000bp (remaining=2706858)
[2026-06-08T08:26:39] Filtering inconsistently clipped mates (remaining=2636632)
[2026-06-08T08:26:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2567971)
[2026-06-08T08:26:43] Filtering fragments with small insert size (remaining=2567232)
[2026-06-08T08:26:44] Filtering alignments with long gaps (remaining=2567232)
[2026-06-08T08:26:45] Filtering fragments with both mates in the same gene (remaining=2566569)
[2026-06-08T08:26:47] Filtering fusions arising from hairpin structures (remaining=2404898)
[2026-06-08T08:26:48] Filtering reads with a mismatch p-value <=0.01 (remaining=998332)
[2026-06-08T08:26:55] Filtering reads with low entropy (k-mer content >=60%) (remaining=392070)
[2026-06-08T08:27:01] Finding fusions and counting supporting reads (total=320231)
[2026-06-08T08:27:11] Merging adjacent fusion breakpoints (remaining=316626)
[2026-06-08T08:27:12] Filtering multi-mapping fusions by alignment score and read support (remaining=184709)
[2026-06-08T08:27:33] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=183942)
[2026-06-08T08:27:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=100196)
[2026-06-08T08:27:37] Filtering fusions with <2 supporting reads (remaining=11722)
[2026-06-08T08:27:38] Filtering fusions with an e-value >=0.3 (remaining=2811)
[2026-06-08T08:27:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2848)
[2026-06-08T08:27:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2780)
[2026-06-08T08:27:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2780)
[2026-06-08T08:27:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2771)
[2026-06-08T08:27:44] Searching for fusions with spliced split reads (remaining=2811)
[2026-06-08T08:27:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=2067)
[2026-06-08T08:27:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2040)
[2026-06-08T08:27:48] Searching for fusions with >=4 spliced events (remaining=2290)
[2026-06-08T08:27:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=717)
[2026-06-08T08:28:04] Filtering fusions with anchors <=23nt (remaining=574)
[2026-06-08T08:28:05] Filtering end-to-end fusions with low support (remaining=554)
[2026-06-08T08:28:05] Filtering fusions with no coverage around the breakpoints (remaining=544)
[2026-06-08T08:28:05] Indexing gene sequences 
[2026-06-08T08:28:08] Filtering genes with >=30% identity (remaining=148)
[2026-06-08T08:28:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=67)
[2026-06-08T08:28:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=67)
[2026-06-08T08:28:10] Searching for additional isoforms (remaining=75)
[2026-06-08T08:28:11] Assigning confidence scores to events 
[2026-06-08T08:28:13] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:28:13] Writing fusions to file 'aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:28:13] Writing discarded fusions to file 'aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:29] Freeing resources
[2026-06-08T08:28:40] Done (elapsed time=00:07:40, CPU time=00:07:40, peak memory=11.4gb)