[2026-06-08T08:54:33] Launching Arriba 2.4.0
[2026-06-08T08:54:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:46] Reading chimeric alignments from '659_cVw-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11767781)
[2026-06-08T09:02:12] Marking multi-mapping alignments (marked=7339362)
[2026-06-08T09:02:16] Detecting strandedness (reverse)
[2026-06-08T09:02:16] Assigning strands to alignments 
[2026-06-08T09:02:19] Annotating alignments 
[2026-06-08T09:02:55] Filtering duplicates (remaining=6281291)
[2026-06-08T09:03:03] 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=6076084)
[2026-06-08T09:03:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6076084)
[2026-06-08T09:03:07] Filtering viral contigs with expression lower than the top 5 (remaining=6076084)
[2026-06-08T09:03:13] Filtering viral contigs with less than 5% coverage (remaining=6076084)
[2026-06-08T09:03:15] Estimating fragment length (mate gap mean=-86.8895, mate gap stddev=32.3568, read length mean=141.943)
[2026-06-08T09:03:15] Filtering read-through fragments with a distance <=10000bp (remaining=5760258)
[2026-06-08T09:03:18] Filtering inconsistently clipped mates (remaining=5701242)
[2026-06-08T09:03:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5484092)
[2026-06-08T09:03:24] Filtering fragments with small insert size (remaining=5483686)
[2026-06-08T09:03:26] Filtering alignments with long gaps (remaining=5483684)
[2026-06-08T09:03:28] Filtering fragments with both mates in the same gene (remaining=5482859)
[2026-06-08T09:03:30] Filtering fusions arising from hairpin structures (remaining=5252107)
[2026-06-08T09:03:33] Filtering reads with a mismatch p-value <=0.01 (remaining=2629420)
[2026-06-08T09:03:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=718144)
[2026-06-08T09:03:56] Finding fusions and counting supporting reads (total=564238)
[2026-06-08T09:04:13] Merging adjacent fusion breakpoints (remaining=560645)
[2026-06-08T09:04:15] Filtering multi-mapping fusions by alignment score and read support (remaining=356284)
[2026-06-08T09:04:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=352407)
[2026-06-08T09:04:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=184638)
[2026-06-08T09:05:00] Filtering fusions with <2 supporting reads (remaining=28778)
[2026-06-08T09:05:01] Filtering fusions with an e-value >=0.3 (remaining=11660)
[2026-06-08T09:05:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11700)
[2026-06-08T09:05:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11584)
[2026-06-08T09:05:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11584)
[2026-06-08T09:05:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7346)
[2026-06-08T09:05:13] Searching for fusions with spliced split reads (remaining=7363)
[2026-06-08T09:05:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=3929)
[2026-06-08T09:05:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3884)
[2026-06-08T09:05:20] Searching for fusions with >=4 spliced events (remaining=4561)
[2026-06-08T09:05:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1494)
[2026-06-08T09:05:37] Filtering fusions with anchors <=23nt (remaining=1068)
[2026-06-08T09:05:38] Filtering end-to-end fusions with low support (remaining=1033)
[2026-06-08T09:05:39] Filtering fusions with no coverage around the breakpoints (remaining=995)
[2026-06-08T09:05:39] Indexing gene sequences 
[2026-06-08T09:05:44] Filtering genes with >=30% identity (remaining=298)
[2026-06-08T09:05:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=139)
[2026-06-08T09:05:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=106)
[2026-06-08T09:05:49] Searching for additional isoforms (remaining=144)
[2026-06-08T09:05:50] Assigning confidence scores to events 
[2026-06-08T09:05:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:53] Writing fusions to file '659_cVw-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:05:55] Writing discarded fusions to file '659_cVw-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:21] Freeing resources
[2026-06-08T09:06:40] Done (elapsed time=00:12:07, CPU time=00:12:05, peak memory=16gb)