[2026-06-08T08:48:20] Launching Arriba 2.4.0
[2026-06-08T08:48:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:34] Reading chimeric alignments from '659_cAd-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=11330684)
[2026-06-08T08:55:00] Marking multi-mapping alignments (marked=7284489)
[2026-06-08T08:55:05] Detecting strandedness (reverse)
[2026-06-08T08:55:05] Assigning strands to alignments 
[2026-06-08T08:55:07] Annotating alignments 
[2026-06-08T08:55:48] Filtering duplicates (remaining=3352132)
[2026-06-08T08:55:54] 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=3150694)
[2026-06-08T08:55:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3150694)
[2026-06-08T08:55:59] Filtering viral contigs with expression lower than the top 5 (remaining=3150694)
[2026-06-08T08:56:04] Filtering viral contigs with less than 5% coverage (remaining=3150694)
[2026-06-08T08:56:06] Estimating fragment length (mate gap mean=-85.7849, mate gap stddev=27.455, read length mean=126.252)
[2026-06-08T08:56:06] Filtering read-through fragments with a distance <=10000bp (remaining=2984216)
[2026-06-08T08:56:09] Filtering inconsistently clipped mates (remaining=2929613)
[2026-06-08T08:56:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2803855)
[2026-06-08T08:56:15] Filtering fragments with small insert size (remaining=2803312)
[2026-06-08T08:56:17] Filtering alignments with long gaps (remaining=2803312)
[2026-06-08T08:56:20] Filtering fragments with both mates in the same gene (remaining=2802643)
[2026-06-08T08:56:22] Filtering fusions arising from hairpin structures (remaining=2681698)
[2026-06-08T08:56:25] Filtering reads with a mismatch p-value <=0.01 (remaining=1067043)
[2026-06-08T08:56:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=414419)
[2026-06-08T08:56:41] Finding fusions and counting supporting reads (total=360453)
[2026-06-08T08:56:56] Merging adjacent fusion breakpoints (remaining=356610)
[2026-06-08T08:56:57] Filtering multi-mapping fusions by alignment score and read support (remaining=199414)
[2026-06-08T08:57:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=198445)
[2026-06-08T08:57:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=108942)
[2026-06-08T08:57:39] Filtering fusions with <2 supporting reads (remaining=11421)
[2026-06-08T08:57:40] Filtering fusions with an e-value >=0.3 (remaining=2813)
[2026-06-08T08:57:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2834)
[2026-06-08T08:57:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2744)
[2026-06-08T08:57:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2746)
[2026-06-08T08:57:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2635)
[2026-06-08T08:57:49] Searching for fusions with spliced split reads (remaining=2667)
[2026-06-08T08:57:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=1975)
[2026-06-08T08:57:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1959)
[2026-06-08T08:57:54] Searching for fusions with >=4 spliced events (remaining=2137)
[2026-06-08T08:57:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=721)
[2026-06-08T08:58:08] Filtering fusions with anchors <=23nt (remaining=583)
[2026-06-08T08:58:08] Filtering end-to-end fusions with low support (remaining=570)
[2026-06-08T08:58:09] Filtering fusions with no coverage around the breakpoints (remaining=550)
[2026-06-08T08:58:09] Indexing gene sequences 
[2026-06-08T08:58:12] Filtering genes with >=30% identity (remaining=200)
[2026-06-08T08:58:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=75)
[2026-06-08T08:58:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=72)
[2026-06-08T08:58:15] Searching for additional isoforms (remaining=85)
[2026-06-08T08:58:16] Assigning confidence scores to events 
[2026-06-08T08:58:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:18] Writing fusions to file '659_cAd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:19] Writing discarded fusions to file '659_cAd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:37] Freeing resources
[2026-06-08T08:58:54] Done (elapsed time=00:10:34, CPU time=00:10:33, peak memory=15.6gb)