[2026-06-08T08:40:13] Launching Arriba 2.4.0
[2026-06-08T08:40:13] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:25] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:29] Reading chimeric alignments from '659_ciZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=11711967)
[2026-06-08T08:47:00] Marking multi-mapping alignments (marked=7656526)
[2026-06-08T08:47:05] Detecting strandedness (reverse)
[2026-06-08T08:47:05] Assigning strands to alignments 
[2026-06-08T08:47:07] Annotating alignments 
[2026-06-08T08:47:43] Filtering duplicates (remaining=3243841)
[2026-06-08T08:47:48] 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=3027980)
[2026-06-08T08:47:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3027980)
[2026-06-08T08:47:53] Filtering viral contigs with expression lower than the top 5 (remaining=3027980)
[2026-06-08T08:47:57] Filtering viral contigs with less than 5% coverage (remaining=3027980)
[2026-06-08T08:47:59] Estimating fragment length (mate gap mean=-85.9965, mate gap stddev=26.9479, read length mean=123.426)
[2026-06-08T08:48:00] Filtering read-through fragments with a distance <=10000bp (remaining=2846164)
[2026-06-08T08:48:02] Filtering inconsistently clipped mates (remaining=2795368)
[2026-06-08T08:48:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2691865)
[2026-06-08T08:48:07] Filtering fragments with small insert size (remaining=2691240)
[2026-06-08T08:48:09] Filtering alignments with long gaps (remaining=2691240)
[2026-06-08T08:48:11] Filtering fragments with both mates in the same gene (remaining=2690553)
[2026-06-08T08:48:13] Filtering fusions arising from hairpin structures (remaining=2580348)
[2026-06-08T08:48:16] Filtering reads with a mismatch p-value <=0.01 (remaining=989550)
[2026-06-08T08:48:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=433082)
[2026-06-08T08:48:31] Finding fusions and counting supporting reads (total=384902)
[2026-06-08T08:48:45] Merging adjacent fusion breakpoints (remaining=380344)
[2026-06-08T08:48:46] Filtering multi-mapping fusions by alignment score and read support (remaining=210395)
[2026-06-08T08:49:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=209506)
[2026-06-08T08:49:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=112550)
[2026-06-08T08:49:25] Filtering fusions with <2 supporting reads (remaining=11511)
[2026-06-08T08:49:25] Filtering fusions with an e-value >=0.3 (remaining=2837)
[2026-06-08T08:49:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2854)
[2026-06-08T08:49:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2792)
[2026-06-08T08:49:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2792)
[2026-06-08T08:49:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2768)
[2026-06-08T08:49:33] Searching for fusions with spliced split reads (remaining=2917)
[2026-06-08T08:49:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=2068)
[2026-06-08T08:49:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2055)
[2026-06-08T08:49:38] Searching for fusions with >=4 spliced events (remaining=2276)
[2026-06-08T08:49:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=816)
[2026-06-08T08:49:52] Filtering fusions with anchors <=23nt (remaining=677)
[2026-06-08T08:49:52] Filtering end-to-end fusions with low support (remaining=646)
[2026-06-08T08:49:52] Filtering fusions with no coverage around the breakpoints (remaining=631)
[2026-06-08T08:49:53] Indexing gene sequences 
[2026-06-08T08:49:55] Filtering genes with >=30% identity (remaining=193)
[2026-06-08T08:49:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=41)
[2026-06-08T08:49:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=38)
[2026-06-08T08:49:58] Searching for additional isoforms (remaining=50)
[2026-06-08T08:49:58] Assigning confidence scores to events 
[2026-06-08T08:50:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:00] Writing fusions to file '659_ciZ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:01] Writing discarded fusions to file '659_ciZ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:16] Freeing resources
[2026-06-08T08:50:33] Done (elapsed time=00:10:20, CPU time=00:10:19, peak memory=16.1gb)