[2026-06-08T08:17:10] Launching Arriba 2.4.0
[2026-06-08T08:17:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:21] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:25] Reading chimeric alignments from '659_dm4-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=8622912)
[2026-06-08T08:21:24] Marking multi-mapping alignments (marked=5767505)
[2026-06-08T08:21:27] Detecting strandedness (reverse)
[2026-06-08T08:21:27] Assigning strands to alignments 
[2026-06-08T08:21:29] Annotating alignments 
[2026-06-08T08:21:58] Filtering duplicates (remaining=3020758)
[2026-06-08T08:22:02] 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=2839472)
[2026-06-08T08:22:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2839472)
[2026-06-08T08:22:06] Filtering viral contigs with expression lower than the top 5 (remaining=2839472)
[2026-06-08T08:22:10] Filtering viral contigs with less than 5% coverage (remaining=2839472)
[2026-06-08T08:22:12] Estimating fragment length (mate gap mean=-88.9273, mate gap stddev=26.316, read length mean=127.958)
[2026-06-08T08:22:12] Filtering read-through fragments with a distance <=10000bp (remaining=2712798)
[2026-06-08T08:22:14] Filtering inconsistently clipped mates (remaining=2653794)
[2026-06-08T08:22:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2498349)
[2026-06-08T08:22:18] Filtering fragments with small insert size (remaining=2497791)
[2026-06-08T08:22:20] Filtering alignments with long gaps (remaining=2497791)
[2026-06-08T08:22:21] Filtering fragments with both mates in the same gene (remaining=2497228)
[2026-06-08T08:22:23] Filtering fusions arising from hairpin structures (remaining=2347010)
[2026-06-08T08:22:24] Filtering reads with a mismatch p-value <=0.01 (remaining=1041137)
[2026-06-08T08:22:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=374871)
[2026-06-08T08:22:38] Finding fusions and counting supporting reads (total=317723)
[2026-06-08T08:22:49] Merging adjacent fusion breakpoints (remaining=315389)
[2026-06-08T08:22:50] Filtering multi-mapping fusions by alignment score and read support (remaining=165569)
[2026-06-08T08:23:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:23:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=164717)
[2026-06-08T08:23:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=99162)
[2026-06-08T08:23:22] Filtering fusions with <2 supporting reads (remaining=10170)
[2026-06-08T08:23:23] Filtering fusions with an e-value >=0.3 (remaining=2462)
[2026-06-08T08:23:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2498)
[2026-06-08T08:23:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2402)
[2026-06-08T08:23:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2403)
[2026-06-08T08:23:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2382)
[2026-06-08T08:23:30] Searching for fusions with spliced split reads (remaining=2536)
[2026-06-08T08:23:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=1860)
[2026-06-08T08:23:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1839)
[2026-06-08T08:23:35] Searching for fusions with >=4 spliced events (remaining=2011)
[2026-06-08T08:23:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=619)
[2026-06-08T08:23:47] Filtering fusions with anchors <=23nt (remaining=550)
[2026-06-08T08:23:47] Filtering end-to-end fusions with low support (remaining=523)
[2026-06-08T08:23:48] Filtering fusions with no coverage around the breakpoints (remaining=500)
[2026-06-08T08:23:48] Indexing gene sequences 
[2026-06-08T08:23:51] Filtering genes with >=30% identity (remaining=200)
[2026-06-08T08:23:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=112)
[2026-06-08T08:23:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=107)
[2026-06-08T08:23:54] Searching for additional isoforms (remaining=122)
[2026-06-08T08:23:55] Assigning confidence scores to events 
[2026-06-08T08:23:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:23:56] Writing fusions to file '659_dm4-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:23:57] Writing discarded fusions to file '659_dm4-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:24:13] Freeing resources
[2026-06-08T08:24:26] Done (elapsed time=00:07:16, CPU time=00:07:15, peak memory=13gb)