[2026-06-04T21:13:57] Launching Arriba 2.4.0
[2026-06-04T21:13:57] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:14:05] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:14:09] Reading chimeric alignments from '659_dc8-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9616823)
[2026-06-04T21:20:43] Marking multi-mapping alignments (marked=5878605)
[2026-06-04T21:20:47] Detecting strandedness (reverse)
[2026-06-04T21:20:47] Assigning strands to alignments 
[2026-06-04T21:20:49] Annotating alignments 
[2026-06-04T21:21:19] Filtering duplicates (remaining=6204823)
[2026-06-04T21:21:26] 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=5925652)
[2026-06-04T21:21:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5925652)
[2026-06-04T21:21:29] Filtering viral contigs with expression lower than the top 5 (remaining=5925652)
[2026-06-04T21:21:34] Filtering viral contigs with less than 5% coverage (remaining=5925652)
[2026-06-04T21:21:36] Estimating fragment length (mate gap mean=-86.4036, mate gap stddev=29.2221, read length mean=133.059)
[2026-06-04T21:21:36] Filtering read-through fragments with a distance <=10000bp (remaining=5532375)
[2026-06-04T21:21:38] Filtering inconsistently clipped mates (remaining=5440289)
[2026-06-04T21:21:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5276375)
[2026-06-04T21:21:44] Filtering fragments with small insert size (remaining=5275595)
[2026-06-04T21:21:46] Filtering alignments with long gaps (remaining=5275594)
[2026-06-04T21:21:48] Filtering fragments with both mates in the same gene (remaining=5274628)
[2026-06-04T21:21:50] Filtering fusions arising from hairpin structures (remaining=4980184)
[2026-06-04T21:21:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2637349)
[2026-06-04T21:22:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=1134446)
[2026-06-04T21:22:18] Finding fusions and counting supporting reads (total=800578)
[2026-06-04T21:22:36] Merging adjacent fusion breakpoints (remaining=792293)
[2026-06-04T21:22:37] Filtering multi-mapping fusions by alignment score and read support (remaining=500044)
[2026-06-04T21:23:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:23:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=496960)
[2026-06-04T21:23:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=266655)
[2026-06-04T21:23:20] Filtering fusions with <2 supporting reads (remaining=41556)
[2026-06-04T21:23:21] Filtering fusions with an e-value >=0.3 (remaining=13054)
[2026-06-04T21:23:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13105)
[2026-06-04T21:23:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12990)
[2026-06-04T21:23:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13000)
[2026-06-04T21:23:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9233)
[2026-06-04T21:23:33] Searching for fusions with spliced split reads (remaining=9367)
[2026-06-04T21:23:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=5367)
[2026-06-04T21:23:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5315)
[2026-06-04T21:23:40] Searching for fusions with >=4 spliced events (remaining=6251)
[2026-06-04T21:23:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2082)
[2026-06-04T21:23:58] Filtering fusions with anchors <=23nt (remaining=1593)
[2026-06-04T21:23:59] Filtering end-to-end fusions with low support (remaining=1543)
[2026-06-04T21:23:59] Filtering fusions with no coverage around the breakpoints (remaining=1505)
[2026-06-04T21:24:00] Indexing gene sequences 
[2026-06-04T21:24:06] Filtering genes with >=30% identity (remaining=471)
[2026-06-04T21:24:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=222)
[2026-06-04T21:24:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-04T21:24:16] Searching for additional isoforms (remaining=260)
[2026-06-04T21:24:18] Assigning confidence scores to events 
[2026-06-04T21:24:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:24:21] Writing fusions to file '659_dc8-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:24:23] Writing discarded fusions to file '659_dc8-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:24:53] Freeing resources
[2026-06-04T21:25:10] Done (elapsed time=00:11:13, CPU time=00:11:12, peak memory=14.3gb)