[2026-06-08T08:47:30] Launching Arriba 2.4.0
[2026-06-08T08:47:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:49] Reading chimeric alignments from '659_ciZ-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=13270511)
[2026-06-08T08:56:09] Marking multi-mapping alignments (marked=8375690)
[2026-06-08T08:56:15] Detecting strandedness (reverse)
[2026-06-08T08:56:15] Assigning strands to alignments 
[2026-06-08T08:56:18] Annotating alignments 
[2026-06-08T08:57:21] Filtering duplicates (remaining=5052258)
[2026-06-08T08:57:29] 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=4848789)
[2026-06-08T08:57:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4848789)
[2026-06-08T08:57:36] Filtering viral contigs with expression lower than the top 5 (remaining=4848789)
[2026-06-08T08:57:42] Filtering viral contigs with less than 5% coverage (remaining=4848789)
[2026-06-08T08:57:46] Estimating fragment length (mate gap mean=-88.1773, mate gap stddev=26.5395, read length mean=128.587)
[2026-06-08T08:57:46] Filtering read-through fragments with a distance <=10000bp (remaining=4541533)
[2026-06-08T08:57:50] Filtering inconsistently clipped mates (remaining=4474958)
[2026-06-08T08:57:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4331492)
[2026-06-08T08:57:58] Filtering fragments with small insert size (remaining=4330594)
[2026-06-08T08:58:02] Filtering alignments with long gaps (remaining=4330594)
[2026-06-08T08:58:05] Filtering fragments with both mates in the same gene (remaining=4329848)
[2026-06-08T08:58:09] Filtering fusions arising from hairpin structures (remaining=4152936)
[2026-06-08T08:58:12] Filtering reads with a mismatch p-value <=0.01 (remaining=1867721)
[2026-06-08T08:58:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=699423)
[2026-06-08T08:58:38] Finding fusions and counting supporting reads (total=581477)
[2026-06-08T08:58:59] Merging adjacent fusion breakpoints (remaining=575660)
[2026-06-08T08:59:00] Filtering multi-mapping fusions by alignment score and read support (remaining=328516)
[2026-06-08T08:59:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=327347)
[2026-06-08T08:59:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=171662)
[2026-06-08T08:59:52] Filtering fusions with <2 supporting reads (remaining=20633)
[2026-06-08T08:59:52] Filtering fusions with an e-value >=0.3 (remaining=4834)
[2026-06-08T08:59:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4865)
[2026-06-08T08:59:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4793)
[2026-06-08T08:59:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4793)
[2026-06-08T08:59:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4729)
[2026-06-08T09:00:05] Searching for fusions with spliced split reads (remaining=4775)
[2026-06-08T09:00:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=3192)
[2026-06-08T09:00:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3173)
[2026-06-08T09:00:12] Searching for fusions with >=4 spliced events (remaining=3785)
[2026-06-08T09:00:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1431)
[2026-06-08T09:00:30] Filtering fusions with anchors <=23nt (remaining=1199)
[2026-06-08T09:00:30] Filtering end-to-end fusions with low support (remaining=1172)
[2026-06-08T09:00:31] Filtering fusions with no coverage around the breakpoints (remaining=1143)
[2026-06-08T09:00:32] Indexing gene sequences 
[2026-06-08T09:00:36] Filtering genes with >=30% identity (remaining=314)
[2026-06-08T09:00:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=60)
[2026-06-08T09:00:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=55)
[2026-06-08T09:00:40] Searching for additional isoforms (remaining=70)
[2026-06-08T09:00:41] Assigning confidence scores to events 
[2026-06-08T09:00:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:45] Writing fusions to file '659_ciZ-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:00:45] Writing discarded fusions to file '659_ciZ-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:12] Freeing resources
[2026-06-08T09:01:34] Done (elapsed time=00:14:04, CPU time=00:14:03, peak memory=17.6gb)