[2026-06-08T09:05:39] Launching Arriba 2.4.0
[2026-06-08T09:05:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:05:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:05:51] Reading chimeric alignments from '659_bGW-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11767296)
[2026-06-08T09:13:05] Marking multi-mapping alignments (marked=7066138)
[2026-06-08T09:13:09] Detecting strandedness (reverse)
[2026-06-08T09:13:09] Assigning strands to alignments 
[2026-06-08T09:13:11] Annotating alignments 
[2026-06-08T09:13:49] Filtering duplicates (remaining=6555334)
[2026-06-08T09:13:57] 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=6355763)
[2026-06-08T09:13:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6355763)
[2026-06-08T09:14:01] Filtering viral contigs with expression lower than the top 5 (remaining=6355763)
[2026-06-08T09:14:07] Filtering viral contigs with less than 5% coverage (remaining=6355763)
[2026-06-08T09:14:10] Estimating fragment length (mate gap mean=-89.3317, mate gap stddev=28.6341, read length mean=137.299)
[2026-06-08T09:14:10] Filtering read-through fragments with a distance <=10000bp (remaining=5903742)
[2026-06-08T09:14:12] Filtering inconsistently clipped mates (remaining=5820216)
[2026-06-08T09:14:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5675764)
[2026-06-08T09:14:18] Filtering fragments with small insert size (remaining=5675034)
[2026-06-08T09:14:21] Filtering alignments with long gaps (remaining=5675034)
[2026-06-08T09:14:23] Filtering fragments with both mates in the same gene (remaining=5674185)
[2026-06-08T09:14:26] Filtering fusions arising from hairpin structures (remaining=5372233)
[2026-06-08T09:14:28] Filtering reads with a mismatch p-value <=0.01 (remaining=2773238)
[2026-06-08T09:14:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=1045362)
[2026-06-08T09:14:53] Finding fusions and counting supporting reads (total=802685)
[2026-06-08T09:15:11] Merging adjacent fusion breakpoints (remaining=794950)
[2026-06-08T09:15:13] Filtering multi-mapping fusions by alignment score and read support (remaining=523059)
[2026-06-08T09:15:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:15:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=520783)
[2026-06-08T09:15:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=256340)
[2026-06-08T09:16:00] Filtering fusions with <2 supporting reads (remaining=38823)
[2026-06-08T09:16:01] Filtering fusions with an e-value >=0.3 (remaining=12437)
[2026-06-08T09:16:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12490)
[2026-06-08T09:16:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12414)
[2026-06-08T09:16:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12417)
[2026-06-08T09:16:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7708)
[2026-06-08T09:16:15] Searching for fusions with spliced split reads (remaining=7838)
[2026-06-08T09:16:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=4738)
[2026-06-08T09:16:21] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4690)
[2026-06-08T09:16:22] Searching for fusions with >=4 spliced events (remaining=5744)
[2026-06-08T09:16:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2170)
[2026-06-08T09:16:37] Filtering fusions with anchors <=23nt (remaining=1813)
[2026-06-08T09:16:38] Filtering end-to-end fusions with low support (remaining=1770)
[2026-06-08T09:16:39] Filtering fusions with no coverage around the breakpoints (remaining=1725)
[2026-06-08T09:16:39] Indexing gene sequences 
[2026-06-08T09:16:46] Filtering genes with >=30% identity (remaining=588)
[2026-06-08T09:16:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=257)
[2026-06-08T09:16:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=212)
[2026-06-08T09:16:55] Searching for additional isoforms (remaining=251)
[2026-06-08T09:16:57] Assigning confidence scores to events 
[2026-06-08T09:17:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:17:00] Writing fusions to file '659_bGW-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:17:02] Writing discarded fusions to file '659_bGW-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:17:31] Freeing resources
[2026-06-08T09:17:51] Done (elapsed time=00:12:12, CPU time=00:12:11, peak memory=16.3gb)