[2026-06-08T08:18:38] Launching Arriba 2.4.0
[2026-06-08T08:18:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:18:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:18:56] Reading chimeric alignments from '659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10182201)
[2026-06-08T08:25:00] Marking multi-mapping alignments (marked=6813279)
[2026-06-08T08:25:04] Detecting strandedness (reverse)
[2026-06-08T08:25:04] Assigning strands to alignments 
[2026-06-08T08:25:06] Annotating alignments 
[2026-06-08T08:25:36] Filtering duplicates (remaining=3923012)
[2026-06-08T08:25:41] 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=3579869)
[2026-06-08T08:25:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3579869)
[2026-06-08T08:25:45] Filtering viral contigs with expression lower than the top 5 (remaining=3579869)
[2026-06-08T08:25:49] Filtering viral contigs with less than 5% coverage (remaining=3579869)
[2026-06-08T08:25:51] Estimating fragment length (mate gap mean=-83.673, mate gap stddev=27.4703, read length mean=120.895)
[2026-06-08T08:25:51] Filtering read-through fragments with a distance <=10000bp (remaining=3437417)
[2026-06-08T08:25:53] Filtering inconsistently clipped mates (remaining=3346086)
[2026-06-08T08:25:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3190434)
[2026-06-08T08:25:58] Filtering fragments with small insert size (remaining=3189518)
[2026-06-08T08:26:00] Filtering alignments with long gaps (remaining=3189518)
[2026-06-08T08:26:02] Filtering fragments with both mates in the same gene (remaining=3188517)
[2026-06-08T08:26:03] Filtering fusions arising from hairpin structures (remaining=2952964)
[2026-06-08T08:26:05] Filtering reads with a mismatch p-value <=0.01 (remaining=1306513)
[2026-06-08T08:26:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=510067)
[2026-06-08T08:26:20] Finding fusions and counting supporting reads (total=413402)
[2026-06-08T08:26:33] Merging adjacent fusion breakpoints (remaining=409974)
[2026-06-08T08:26:34] Filtering multi-mapping fusions by alignment score and read support (remaining=226833)
[2026-06-08T08:27:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=225496)
[2026-06-08T08:27:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=133325)
[2026-06-08T08:27:06] Filtering fusions with <2 supporting reads (remaining=11906)
[2026-06-08T08:27:06] Filtering fusions with an e-value >=0.3 (remaining=3015)
[2026-06-08T08:27:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3068)
[2026-06-08T08:27:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2923)
[2026-06-08T08:27:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2923)
[2026-06-08T08:27:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2858)
[2026-06-08T08:27:15] Searching for fusions with spliced split reads (remaining=2908)
[2026-06-08T08:27:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=2160)
[2026-06-08T08:27:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2140)
[2026-06-08T08:27:20] Searching for fusions with >=4 spliced events (remaining=2370)
[2026-06-08T08:27:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=805)
[2026-06-08T08:27:33] Filtering fusions with anchors <=23nt (remaining=652)
[2026-06-08T08:27:34] Filtering end-to-end fusions with low support (remaining=627)
[2026-06-08T08:27:34] Filtering fusions with no coverage around the breakpoints (remaining=607)
[2026-06-08T08:27:34] Indexing gene sequences 
[2026-06-08T08:27:38] Filtering genes with >=30% identity (remaining=258)
[2026-06-08T08:27:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=150)
[2026-06-08T08:27:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-08T08:27:48] Searching for additional isoforms (remaining=147)
[2026-06-08T08:27:48] Assigning confidence scores to events 
[2026-06-08T08:27:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:27:50] Writing fusions to file '659_bCu-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:27:51] Writing discarded fusions to file '659_bCu-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:09] Freeing resources
[2026-06-08T08:28:23] Done (elapsed time=00:09:45, CPU time=00:09:44, peak memory=14.6gb)