[2026-06-08T08:58:30] Launching Arriba 2.4.0
[2026-06-08T08:58:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:58:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:43] Reading chimeric alignments from '659_bTo-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11363217)
[2026-06-08T09:06:06] Marking multi-mapping alignments (marked=6631159)
[2026-06-08T09:06:10] Detecting strandedness (reverse)
[2026-06-08T09:06:10] Assigning strands to alignments 
[2026-06-08T09:06:13] Annotating alignments 
[2026-06-08T09:06:52] Filtering duplicates (remaining=6047960)
[2026-06-08T09:07:00] 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=5937431)
[2026-06-08T09:07:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5937431)
[2026-06-08T09:07:04] Filtering viral contigs with expression lower than the top 5 (remaining=5937431)
[2026-06-08T09:07:10] Filtering viral contigs with less than 5% coverage (remaining=5937431)
[2026-06-08T09:07:12] Estimating fragment length (mate gap mean=-87.8432, mate gap stddev=30.176, read length mean=139.709)
[2026-06-08T09:07:12] Filtering read-through fragments with a distance <=10000bp (remaining=5636671)
[2026-06-08T09:07:15] Filtering inconsistently clipped mates (remaining=5575981)
[2026-06-08T09:07:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5424384)
[2026-06-08T09:07:21] Filtering fragments with small insert size (remaining=5423817)
[2026-06-08T09:07:24] Filtering alignments with long gaps (remaining=5423817)
[2026-06-08T09:07:26] Filtering fragments with both mates in the same gene (remaining=5423038)
[2026-06-08T09:07:28] Filtering fusions arising from hairpin structures (remaining=5188997)
[2026-06-08T09:07:31] Filtering reads with a mismatch p-value <=0.01 (remaining=2591439)
[2026-06-08T09:07:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=795243)
[2026-06-08T09:07:55] Finding fusions and counting supporting reads (total=627669)
[2026-06-08T09:08:13] Merging adjacent fusion breakpoints (remaining=622417)
[2026-06-08T09:08:14] Filtering multi-mapping fusions by alignment score and read support (remaining=439835)
[2026-06-08T09:08:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:08:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=438098)
[2026-06-08T09:09:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=212525)
[2026-06-08T09:09:01] Filtering fusions with <2 supporting reads (remaining=32631)
[2026-06-08T09:09:02] Filtering fusions with an e-value >=0.3 (remaining=11615)
[2026-06-08T09:09:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11655)
[2026-06-08T09:09:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11588)
[2026-06-08T09:09:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11588)
[2026-06-08T09:09:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5801)
[2026-06-08T09:09:14] Searching for fusions with spliced split reads (remaining=5929)
[2026-06-08T09:09:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=3711)
[2026-06-08T09:09:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3675)
[2026-06-08T09:09:21] Searching for fusions with >=4 spliced events (remaining=4530)
[2026-06-08T09:09:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1722)
[2026-06-08T09:09:35] Filtering fusions with anchors <=23nt (remaining=1440)
[2026-06-08T09:09:36] Filtering end-to-end fusions with low support (remaining=1405)
[2026-06-08T09:09:37] Filtering fusions with no coverage around the breakpoints (remaining=1370)
[2026-06-08T09:09:37] Indexing gene sequences 
[2026-06-08T09:09:43] Filtering genes with >=30% identity (remaining=415)
[2026-06-08T09:09:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-06-08T09:09:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-08T09:09:51] Searching for additional isoforms (remaining=200)
[2026-06-08T09:09:52] Assigning confidence scores to events 
[2026-06-08T09:09:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:55] Writing fusions to file '659_bTo-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:09:57] Writing discarded fusions to file '659_bTo-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:25] Freeing resources
[2026-06-08T09:10:46] Done (elapsed time=00:12:16, CPU time=00:12:14, peak memory=15.6gb)