[2026-06-08T08:51:37] Launching Arriba 2.4.0
[2026-06-08T08:51:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:53] Reading chimeric alignments from '659_dc8-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=12205262)
[2026-06-08T08:59:26] Marking multi-mapping alignments (marked=7460490)
[2026-06-08T08:59:32] Detecting strandedness (reverse)
[2026-06-08T08:59:32] Assigning strands to alignments 
[2026-06-08T08:59:34] Annotating alignments 
[2026-06-08T09:00:26] Filtering duplicates (remaining=6224448)
[2026-06-08T09:00:39] 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=6022663)
[2026-06-08T09:00:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6022663)
[2026-06-08T09:00:48] Filtering viral contigs with expression lower than the top 5 (remaining=6022663)
[2026-06-08T09:00:54] Filtering viral contigs with less than 5% coverage (remaining=6022663)
[2026-06-08T09:00:58] Estimating fragment length (mate gap mean=-88.2964, mate gap stddev=30.5635, read length mean=139.243)
[2026-06-08T09:00:58] Filtering read-through fragments with a distance <=10000bp (remaining=5675875)
[2026-06-08T09:01:01] Filtering inconsistently clipped mates (remaining=5606218)
[2026-06-08T09:01:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5429086)
[2026-06-08T09:01:10] Filtering fragments with small insert size (remaining=5428528)
[2026-06-08T09:01:12] Filtering alignments with long gaps (remaining=5428528)
[2026-06-08T09:01:15] Filtering fragments with both mates in the same gene (remaining=5427678)
[2026-06-08T09:01:18] Filtering fusions arising from hairpin structures (remaining=5179058)
[2026-06-08T09:01:21] Filtering reads with a mismatch p-value <=0.01 (remaining=2558783)
[2026-06-08T09:01:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=848279)
[2026-06-08T09:01:47] Finding fusions and counting supporting reads (total=669809)
[2026-06-08T09:02:07] Merging adjacent fusion breakpoints (remaining=663578)
[2026-06-08T09:02:09] Filtering multi-mapping fusions by alignment score and read support (remaining=409608)
[2026-06-08T09:02:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=405723)
[2026-06-08T09:02:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=213056)
[2026-06-08T09:03:00] Filtering fusions with <2 supporting reads (remaining=33277)
[2026-06-08T09:03:01] Filtering fusions with an e-value >=0.3 (remaining=11860)
[2026-06-08T09:03:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11907)
[2026-06-08T09:03:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11787)
[2026-06-08T09:03:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11799)
[2026-06-08T09:03:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7677)
[2026-06-08T09:03:15] Searching for fusions with spliced split reads (remaining=7810)
[2026-06-08T09:03:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4681)
[2026-06-08T09:03:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4632)
[2026-06-08T09:03:24] Searching for fusions with >=4 spliced events (remaining=5426)
[2026-06-08T09:03:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1803)
[2026-06-08T09:03:45] Filtering fusions with anchors <=23nt (remaining=1339)
[2026-06-08T09:03:46] Filtering end-to-end fusions with low support (remaining=1297)
[2026-06-08T09:03:47] Filtering fusions with no coverage around the breakpoints (remaining=1260)
[2026-06-08T09:03:48] Indexing gene sequences 
[2026-06-08T09:03:54] Filtering genes with >=30% identity (remaining=385)
[2026-06-08T09:03:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=188)
[2026-06-08T09:04:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=159)
[2026-06-08T09:04:03] Searching for additional isoforms (remaining=208)
[2026-06-08T09:04:04] Assigning confidence scores to events 
[2026-06-08T09:04:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:09] Writing fusions to file '659_dc8-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:04:11] Writing discarded fusions to file '659_dc8-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:46] Freeing resources
[2026-06-08T09:05:09] Done (elapsed time=00:13:32, CPU time=00:13:31, peak memory=16.5gb)