[2026-06-08T09:11:33] Launching Arriba 2.4.0
[2026-06-08T09:11:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:11:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:11:46] Reading chimeric alignments from '659_cTi-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11643718)
[2026-06-08T09:19:03] Marking multi-mapping alignments (marked=6742640)
[2026-06-08T09:19:09] Detecting strandedness (reverse)
[2026-06-08T09:19:09] Assigning strands to alignments 
[2026-06-08T09:19:12] Annotating alignments 
[2026-06-08T09:19:51] Filtering duplicates (remaining=6193512)
[2026-06-08T09:19:58] 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=6064398)
[2026-06-08T09:20:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6064398)
[2026-06-08T09:20:03] Filtering viral contigs with expression lower than the top 5 (remaining=6064398)
[2026-06-08T09:20:08] Filtering viral contigs with less than 5% coverage (remaining=6064398)
[2026-06-08T09:20:10] Estimating fragment length (mate gap mean=-91.1761, mate gap stddev=29.8191, read length mean=139.924)
[2026-06-08T09:20:10] Filtering read-through fragments with a distance <=10000bp (remaining=5633998)
[2026-06-08T09:20:13] Filtering inconsistently clipped mates (remaining=5564507)
[2026-06-08T09:20:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5405382)
[2026-06-08T09:20:19] Filtering fragments with small insert size (remaining=5404829)
[2026-06-08T09:20:21] Filtering alignments with long gaps (remaining=5404828)
[2026-06-08T09:20:23] Filtering fragments with both mates in the same gene (remaining=5404014)
[2026-06-08T09:20:25] Filtering fusions arising from hairpin structures (remaining=5166513)
[2026-06-08T09:20:28] Filtering reads with a mismatch p-value <=0.01 (remaining=2587125)
[2026-06-08T09:20:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=947151)
[2026-06-08T09:20:51] Finding fusions and counting supporting reads (total=744422)
[2026-06-08T09:21:08] Merging adjacent fusion breakpoints (remaining=737169)
[2026-06-08T09:21:10] Filtering multi-mapping fusions by alignment score and read support (remaining=490852)
[2026-06-08T09:21:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:21:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=488294)
[2026-06-08T09:21:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=237864)
[2026-06-08T09:21:54] Filtering fusions with <2 supporting reads (remaining=35082)
[2026-06-08T09:21:55] Filtering fusions with an e-value >=0.3 (remaining=10648)
[2026-06-08T09:21:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10686)
[2026-06-08T09:21:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10585)
[2026-06-08T09:22:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10586)
[2026-06-08T09:22:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8450)
[2026-06-08T09:22:07] Searching for fusions with spliced split reads (remaining=8575)
[2026-06-08T09:22:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=5126)
[2026-06-08T09:22:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5046)
[2026-06-08T09:22:14] Searching for fusions with >=4 spliced events (remaining=6142)
[2026-06-08T09:22:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2359)
[2026-06-08T09:22:34] Filtering fusions with anchors <=23nt (remaining=1793)
[2026-06-08T09:22:35] Filtering end-to-end fusions with low support (remaining=1747)
[2026-06-08T09:22:35] Filtering fusions with no coverage around the breakpoints (remaining=1693)
[2026-06-08T09:22:36] Indexing gene sequences 
[2026-06-08T09:22:42] Filtering genes with >=30% identity (remaining=548)
[2026-06-08T09:22:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=243)
[2026-06-08T09:22:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=195)
[2026-06-08T09:22:51] Searching for additional isoforms (remaining=251)
[2026-06-08T09:22:53] Assigning confidence scores to events 
[2026-06-08T09:22:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:22:56] Writing fusions to file '659_cTi-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:22:58] Writing discarded fusions to file '659_cTi-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:23:25] Freeing resources
[2026-06-08T09:23:45] Done (elapsed time=00:12:12, CPU time=00:12:11, peak memory=16.2gb)