[2026-06-08T08:50:20] Launching Arriba 2.4.0
[2026-06-08T08:50:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:32] Reading chimeric alignments from '659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=8674090)
[2026-06-08T08:57:26] Marking multi-mapping alignments (marked=5270931)
[2026-06-08T08:57:29] Detecting strandedness (reverse)
[2026-06-08T08:57:29] Assigning strands to alignments 
[2026-06-08T08:57:31] Annotating alignments 
[2026-06-08T08:57:57] Filtering duplicates (remaining=3467200)
[2026-06-08T08:58:01] 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=3295425)
[2026-06-08T08:58:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3295425)
[2026-06-08T08:58:04] Filtering viral contigs with expression lower than the top 5 (remaining=3295425)
[2026-06-08T08:58:08] Filtering viral contigs with less than 5% coverage (remaining=3295425)
[2026-06-08T08:58:10] Estimating fragment length (mate gap mean=-87.7451, mate gap stddev=29.7737, read length mean=135.935)
[2026-06-08T08:58:10] Filtering read-through fragments with a distance <=10000bp (remaining=3117928)
[2026-06-08T08:58:11] Filtering inconsistently clipped mates (remaining=3065743)
[2026-06-08T08:58:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2954417)
[2026-06-08T08:58:16] Filtering fragments with small insert size (remaining=2953920)
[2026-06-08T08:58:17] Filtering alignments with long gaps (remaining=2953920)
[2026-06-08T08:58:19] Filtering fragments with both mates in the same gene (remaining=2953240)
[2026-06-08T08:58:20] Filtering fusions arising from hairpin structures (remaining=2783361)
[2026-06-08T08:58:22] Filtering reads with a mismatch p-value <=0.01 (remaining=1170259)
[2026-06-08T08:58:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=429251)
[2026-06-08T08:58:36] Finding fusions and counting supporting reads (total=334760)
[2026-06-08T08:58:47] Merging adjacent fusion breakpoints (remaining=331204)
[2026-06-08T08:58:47] Filtering multi-mapping fusions by alignment score and read support (remaining=217740)
[2026-06-08T08:59:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=215867)
[2026-06-08T08:59:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=113332)
[2026-06-08T08:59:17] Filtering fusions with <2 supporting reads (remaining=17153)
[2026-06-08T08:59:18] Filtering fusions with an e-value >=0.3 (remaining=5581)
[2026-06-08T08:59:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5608)
[2026-06-08T08:59:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5545)
[2026-06-08T08:59:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5546)
[2026-06-08T08:59:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3515)
[2026-06-08T08:59:25] Searching for fusions with spliced split reads (remaining=3597)
[2026-06-08T08:59:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=2513)
[2026-06-08T08:59:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2484)
[2026-06-08T08:59:30] Searching for fusions with >=4 spliced events (remaining=2694)
[2026-06-08T08:59:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=663)
[2026-06-08T08:59:43] Filtering fusions with anchors <=23nt (remaining=510)
[2026-06-08T08:59:43] Filtering end-to-end fusions with low support (remaining=493)
[2026-06-08T08:59:44] Filtering fusions with no coverage around the breakpoints (remaining=473)
[2026-06-08T08:59:44] Indexing gene sequences 
[2026-06-08T08:59:47] Filtering genes with >=30% identity (remaining=194)
[2026-06-08T08:59:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=123)
[2026-06-08T08:59:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=110)
[2026-06-08T08:59:50] Searching for additional isoforms (remaining=130)
[2026-06-08T08:59:51] Assigning confidence scores to events 
[2026-06-08T08:59:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:53] Writing fusions to file '659_bhK-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:54] Writing discarded fusions to file '659_bhK-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:09] Freeing resources
[2026-06-08T09:00:23] Done (elapsed time=00:10:03, CPU time=00:10:02, peak memory=13gb)