[2026-06-08T09:00:34] Launching Arriba 2.4.0
[2026-06-08T09:00:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:00:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:00:48] Reading chimeric alignments from '659_bUW-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11959686)
[2026-06-08T09:09:12] Marking multi-mapping alignments (marked=7574827)
[2026-06-08T09:09:17] Detecting strandedness (reverse)
[2026-06-08T09:09:17] Assigning strands to alignments 
[2026-06-08T09:09:20] Annotating alignments 
[2026-06-08T09:10:01] Filtering duplicates (remaining=7553311)
[2026-06-08T09:10:09] 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=7417407)
[2026-06-08T09:10:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7417407)
[2026-06-08T09:10:14] Filtering viral contigs with expression lower than the top 5 (remaining=7417407)
[2026-06-08T09:10:20] Filtering viral contigs with less than 5% coverage (remaining=7417407)
[2026-06-08T09:10:23] Estimating fragment length (mate gap mean=-88.9491, mate gap stddev=29.4396, read length mean=140.487)
[2026-06-08T09:10:23] Filtering read-through fragments with a distance <=10000bp (remaining=6861473)
[2026-06-08T09:10:25] Filtering inconsistently clipped mates (remaining=6786547)
[2026-06-08T09:10:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6607353)
[2026-06-08T09:10:33] Filtering fragments with small insert size (remaining=6606941)
[2026-06-08T09:10:35] Filtering alignments with long gaps (remaining=6606941)
[2026-06-08T09:10:38] Filtering fragments with both mates in the same gene (remaining=6606098)
[2026-06-08T09:10:41] Filtering fusions arising from hairpin structures (remaining=6265680)
[2026-06-08T09:10:44] Filtering reads with a mismatch p-value <=0.01 (remaining=3214634)
[2026-06-08T09:11:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=1173486)
[2026-06-08T09:11:14] Finding fusions and counting supporting reads (total=852390)
[2026-06-08T09:11:35] Merging adjacent fusion breakpoints (remaining=841979)
[2026-06-08T09:11:37] Filtering multi-mapping fusions by alignment score and read support (remaining=544007)
[2026-06-08T09:12:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:12:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=542018)
[2026-06-08T09:12:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=249261)
[2026-06-08T09:12:30] Filtering fusions with <2 supporting reads (remaining=37737)
[2026-06-08T09:12:31] Filtering fusions with an e-value >=0.3 (remaining=12703)
[2026-06-08T09:12:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12740)
[2026-06-08T09:12:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12645)
[2026-06-08T09:12:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12647)
[2026-06-08T09:12:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9235)
[2026-06-08T09:12:45] Searching for fusions with spliced split reads (remaining=9249)
[2026-06-08T09:12:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=4877)
[2026-06-08T09:12:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4841)
[2026-06-08T09:12:53] Searching for fusions with >=4 spliced events (remaining=6011)
[2026-06-08T09:12:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2440)
[2026-06-08T09:13:09] Filtering fusions with anchors <=23nt (remaining=1955)
[2026-06-08T09:13:10] Filtering end-to-end fusions with low support (remaining=1905)
[2026-06-08T09:13:11] Filtering fusions with no coverage around the breakpoints (remaining=1865)
[2026-06-08T09:13:11] Indexing gene sequences 
[2026-06-08T09:13:18] Filtering genes with >=30% identity (remaining=509)
[2026-06-08T09:13:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=168)
[2026-06-08T09:13:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=141)
[2026-06-08T09:13:25] Searching for additional isoforms (remaining=218)
[2026-06-08T09:13:27] Assigning confidence scores to events 
[2026-06-08T09:13:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:13:31] Writing fusions to file '659_bUW-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:13:34] Writing discarded fusions to file '659_bUW-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:14:08] Freeing resources
[2026-06-08T09:14:29] Done (elapsed time=00:13:55, CPU time=00:13:53, peak memory=16.4gb)