[2026-06-08T09:12:22] Launching Arriba 2.4.0
[2026-06-08T09:12:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:12:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:12:35] Reading chimeric alignments from '659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9759402)
[2026-06-08T09:19:28] Marking multi-mapping alignments (marked=5956784)
[2026-06-08T09:19:32] Detecting strandedness (reverse)
[2026-06-08T09:19:32] Assigning strands to alignments 
[2026-06-08T09:19:34] Annotating alignments 
[2026-06-08T09:20:07] Filtering duplicates (remaining=4736020)
[2026-06-08T09:20:13] 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=4521294)
[2026-06-08T09:20:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4521294)
[2026-06-08T09:20:16] Filtering viral contigs with expression lower than the top 5 (remaining=4521294)
[2026-06-08T09:20:21] Filtering viral contigs with less than 5% coverage (remaining=4521294)
[2026-06-08T09:20:23] Estimating fragment length (mate gap mean=-87.6106, mate gap stddev=30.0472, read length mean=136.958)
[2026-06-08T09:20:23] Filtering read-through fragments with a distance <=10000bp (remaining=4270550)
[2026-06-08T09:20:25] Filtering inconsistently clipped mates (remaining=4210984)
[2026-06-08T09:20:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4080570)
[2026-06-08T09:20:30] Filtering fragments with small insert size (remaining=4080071)
[2026-06-08T09:20:32] Filtering alignments with long gaps (remaining=4080071)
[2026-06-08T09:20:34] Filtering fragments with both mates in the same gene (remaining=4079396)
[2026-06-08T09:20:35] Filtering fusions arising from hairpin structures (remaining=3879232)
[2026-06-08T09:20:37] Filtering reads with a mismatch p-value <=0.01 (remaining=1640017)
[2026-06-08T09:20:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=646272)
[2026-06-08T09:20:56] Finding fusions and counting supporting reads (total=513833)
[2026-06-08T09:21:09] Merging adjacent fusion breakpoints (remaining=508510)
[2026-06-08T09:21:11] Filtering multi-mapping fusions by alignment score and read support (remaining=352520)
[2026-06-08T09:21:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:21:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=351019)
[2026-06-08T09:21:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=175620)
[2026-06-08T09:21:49] Filtering fusions with <2 supporting reads (remaining=27301)
[2026-06-08T09:21:50] Filtering fusions with an e-value >=0.3 (remaining=9790)
[2026-06-08T09:21:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9823)
[2026-06-08T09:21:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9754)
[2026-06-08T09:21:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9754)
[2026-06-08T09:21:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5044)
[2026-06-08T09:22:00] Searching for fusions with spliced split reads (remaining=5158)
[2026-06-08T09:22:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=3281)
[2026-06-08T09:22:06] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3256)
[2026-06-08T09:22:06] Searching for fusions with >=4 spliced events (remaining=3782)
[2026-06-08T09:22:08] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1354)
[2026-06-08T09:22:21] Filtering fusions with anchors <=23nt (remaining=1054)
[2026-06-08T09:22:21] Filtering end-to-end fusions with low support (remaining=1012)
[2026-06-08T09:22:22] Filtering fusions with no coverage around the breakpoints (remaining=985)
[2026-06-08T09:22:23] Indexing gene sequences 
[2026-06-08T09:22:27] Filtering genes with >=30% identity (remaining=337)
[2026-06-08T09:22:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=177)
[2026-06-08T09:22:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=161)
[2026-06-08T09:22:32] Searching for additional isoforms (remaining=192)
[2026-06-08T09:22:34] Assigning confidence scores to events 
[2026-06-08T09:22:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:22:36] Writing fusions to file '659_bTo-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:22:37] Writing discarded fusions to file '659_bTo-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:23:01] Freeing resources
[2026-06-08T09:23:17] Done (elapsed time=00:10:55, CPU time=00:10:54, peak memory=14.3gb)