[2026-06-08T08:31:50] Launching Arriba 2.4.0
[2026-06-08T08:31:50] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:02] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:06] Reading chimeric alignments from '659_On-T1-TRNA-2_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10546263)
[2026-06-08T08:38:41] Marking multi-mapping alignments (marked=6458619)
[2026-06-08T08:38:45] Detecting strandedness (reverse)
[2026-06-08T08:38:45] Assigning strands to alignments 
[2026-06-08T08:38:47] Annotating alignments 
[2026-06-08T08:39:16] Filtering duplicates (remaining=7244361)
[2026-06-08T08:39:23] 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=6997704)
[2026-06-08T08:39:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6997704)
[2026-06-08T08:39:26] Filtering viral contigs with expression lower than the top 5 (remaining=6997704)
[2026-06-08T08:39:31] Filtering viral contigs with less than 5% coverage (remaining=6997704)
[2026-06-08T08:39:33] Estimating fragment length (mate gap mean=-85.0464, mate gap stddev=29.5513, read length mean=132.638)
[2026-06-08T08:39:33] Filtering read-through fragments with a distance <=10000bp (remaining=6583669)
[2026-06-08T08:39:35] Filtering inconsistently clipped mates (remaining=6479993)
[2026-06-08T08:39:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6262886)
[2026-06-08T08:39:40] Filtering fragments with small insert size (remaining=6261902)
[2026-06-08T08:39:42] Filtering alignments with long gaps (remaining=6261901)
[2026-06-08T08:39:44] Filtering fragments with both mates in the same gene (remaining=6260676)
[2026-06-08T08:39:46] Filtering fusions arising from hairpin structures (remaining=5892276)
[2026-06-08T08:39:48] Filtering reads with a mismatch p-value <=0.01 (remaining=3231574)
[2026-06-08T08:40:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=1282920)
[2026-06-08T08:40:14] Finding fusions and counting supporting reads (total=937483)
[2026-06-08T08:40:29] Merging adjacent fusion breakpoints (remaining=928102)
[2026-06-08T08:40:31] Filtering multi-mapping fusions by alignment score and read support (remaining=575864)
[2026-06-08T08:40:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=571810)
[2026-06-08T08:41:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=314853)
[2026-06-08T08:41:07] Filtering fusions with <2 supporting reads (remaining=41484)
[2026-06-08T08:41:08] Filtering fusions with an e-value >=0.3 (remaining=12006)
[2026-06-08T08:41:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12049)
[2026-06-08T08:41:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11927)
[2026-06-08T08:41:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11933)
[2026-06-08T08:41:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8266)
[2026-06-08T08:41:19] Searching for fusions with spliced split reads (remaining=8287)
[2026-06-08T08:41:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=4937)
[2026-06-08T08:41:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4877)
[2026-06-08T08:41:26] Searching for fusions with >=4 spliced events (remaining=6076)
[2026-06-08T08:41:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2357)
[2026-06-08T08:41:40] Filtering fusions with anchors <=23nt (remaining=1893)
[2026-06-08T08:41:41] Filtering end-to-end fusions with low support (remaining=1838)
[2026-06-08T08:41:42] Filtering fusions with no coverage around the breakpoints (remaining=1793)
[2026-06-08T08:41:42] Indexing gene sequences 
[2026-06-08T08:41:48] Filtering genes with >=30% identity (remaining=516)
[2026-06-08T08:41:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=242)
[2026-06-08T08:41:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=203)
[2026-06-08T08:41:59] Searching for additional isoforms (remaining=267)
[2026-06-08T08:42:00] Assigning confidence scores to events 
[2026-06-08T08:42:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:03] Writing fusions to file '659_On-T1-TRNA-2_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:05] Writing discarded fusions to file '659_On-T1-TRNA-2_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:33] Freeing resources
[2026-06-08T08:42:51] Done (elapsed time=00:11:01, CPU time=00:11:00, peak memory=15.1gb)