[2026-06-08T07:53:58] Launching Arriba 2.4.0
[2026-06-08T07:53:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:54:15] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:54:21] Reading chimeric alignments from '659_dcz-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=4826136)
[2026-06-08T07:57:38] Marking multi-mapping alignments (marked=3257924)
[2026-06-08T07:57:41] Detecting strandedness (reverse)
[2026-06-08T07:57:41] Assigning strands to alignments 
[2026-06-08T07:57:42] Annotating alignments 
[2026-06-08T07:58:02] Filtering duplicates (remaining=1587297)
[2026-06-08T07:58:05] 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=1514365)
[2026-06-08T07:58:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1514365)
[2026-06-08T07:58:07] Filtering viral contigs with expression lower than the top 5 (remaining=1514365)
[2026-06-08T07:58:09] Filtering viral contigs with less than 5% coverage (remaining=1514365)
[2026-06-08T07:58:11] Estimating fragment length (mate gap mean=-86.7833, mate gap stddev=26.3141, read length mean=124.891)
[2026-06-08T07:58:11] Filtering read-through fragments with a distance <=10000bp (remaining=1448587)
[2026-06-08T07:58:12] Filtering inconsistently clipped mates (remaining=1415803)
[2026-06-08T07:58:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1325372)
[2026-06-08T07:58:15] Filtering fragments with small insert size (remaining=1324943)
[2026-06-08T07:58:16] Filtering alignments with long gaps (remaining=1324943)
[2026-06-08T07:58:17] Filtering fragments with both mates in the same gene (remaining=1324605)
[2026-06-08T07:58:18] Filtering fusions arising from hairpin structures (remaining=1253263)
[2026-06-08T07:58:19] Filtering reads with a mismatch p-value <=0.01 (remaining=513791)
[2026-06-08T07:58:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=174862)
[2026-06-08T07:58:26] Finding fusions and counting supporting reads (total=167404)
[2026-06-08T07:58:34] Merging adjacent fusion breakpoints (remaining=166608)
[2026-06-08T07:58:34] Filtering multi-mapping fusions by alignment score and read support (remaining=79945)
[2026-06-08T07:58:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:58:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=79450)
[2026-06-08T07:58:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=49736)
[2026-06-08T07:58:58] Filtering fusions with <2 supporting reads (remaining=3412)
[2026-06-08T07:58:58] Filtering fusions with an e-value >=0.3 (remaining=915)
[2026-06-08T07:58:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=936)
[2026-06-08T07:59:00] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=893)
[2026-06-08T07:59:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=894)
[2026-06-08T07:59:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=884)
[2026-06-08T07:59:03] Searching for fusions with spliced split reads (remaining=938)
[2026-06-08T07:59:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=746)
[2026-06-08T07:59:06] Filtering read-through fusions with breakpoints near the gene boundary (remaining=738)
[2026-06-08T07:59:06] Searching for fusions with >=4 spliced events (remaining=794)
[2026-06-08T07:59:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=270)
[2026-06-08T07:59:26] Filtering fusions with anchors <=23nt (remaining=241)
[2026-06-08T07:59:26] Filtering end-to-end fusions with low support (remaining=233)
[2026-06-08T07:59:26] Filtering fusions with no coverage around the breakpoints (remaining=217)
[2026-06-08T07:59:27] Indexing gene sequences 
[2026-06-08T07:59:29] Filtering genes with >=30% identity (remaining=87)
[2026-06-08T07:59:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=52)
[2026-06-08T07:59:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=52)
[2026-06-08T07:59:30] Searching for additional isoforms (remaining=61)
[2026-06-08T07:59:31] Assigning confidence scores to events 
[2026-06-08T07:59:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:59:32] Writing fusions to file '659_dcz-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:59:33] Writing discarded fusions to file '659_dcz-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:59:45] Freeing resources
[2026-06-08T07:59:57] Done (elapsed time=00:05:59, CPU time=00:05:58, peak memory=9.01gb)