[2026-06-08T09:13:55] Launching Arriba 2.4.0
[2026-06-08T09:13:55] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:14:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:14:10] Reading chimeric alignments from '659_ezg-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=12421533)
[2026-06-08T09:21:47] Marking multi-mapping alignments (marked=7717023)
[2026-06-08T09:21:52] Detecting strandedness (reverse)
[2026-06-08T09:21:52] Assigning strands to alignments 
[2026-06-08T09:21:55] Annotating alignments 
[2026-06-08T09:22:36] Filtering duplicates (remaining=7768384)
[2026-06-08T09:22:45] 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=7544890)
[2026-06-08T09:22:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7544890)
[2026-06-08T09:22:50] Filtering viral contigs with expression lower than the top 5 (remaining=7544890)
[2026-06-08T09:22:56] Filtering viral contigs with less than 5% coverage (remaining=7544890)
[2026-06-08T09:22:58] Estimating fragment length (mate gap mean=-89.318, mate gap stddev=28.0052, read length mean=134.684)
[2026-06-08T09:22:59] Filtering read-through fragments with a distance <=10000bp (remaining=6991171)
[2026-06-08T09:23:01] Filtering inconsistently clipped mates (remaining=6884969)
[2026-06-08T09:23:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6712265)
[2026-06-08T09:23:09] Filtering fragments with small insert size (remaining=6711409)
[2026-06-08T09:23:11] Filtering alignments with long gaps (remaining=6711409)
[2026-06-08T09:23:14] Filtering fragments with both mates in the same gene (remaining=6710379)
[2026-06-08T09:23:16] Filtering fusions arising from hairpin structures (remaining=6324219)
[2026-06-08T09:23:19] Filtering reads with a mismatch p-value <=0.01 (remaining=3329529)
[2026-06-08T09:23:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=1357708)
[2026-06-08T09:23:51] Finding fusions and counting supporting reads (total=1051884)
[2026-06-08T09:24:13] Merging adjacent fusion breakpoints (remaining=1039537)
[2026-06-08T09:24:16] Filtering multi-mapping fusions by alignment score and read support (remaining=649583)
[2026-06-08T09:24:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:25:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=647142)
[2026-06-08T09:25:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=348117)
[2026-06-08T09:25:10] Filtering fusions with <2 supporting reads (remaining=44977)
[2026-06-08T09:25:11] Filtering fusions with an e-value >=0.3 (remaining=10966)
[2026-06-08T09:25:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11025)
[2026-06-08T09:25:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10880)
[2026-06-08T09:25:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10885)
[2026-06-08T09:25:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8731)
[2026-06-08T09:25:26] Searching for fusions with spliced split reads (remaining=8739)
[2026-06-08T09:25:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=5312)
[2026-06-08T09:25:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5268)
[2026-06-08T09:25:35] Searching for fusions with >=4 spliced events (remaining=6678)
[2026-06-08T09:25:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2788)
[2026-06-08T09:25:52] Filtering fusions with anchors <=23nt (remaining=2309)
[2026-06-08T09:25:53] Filtering end-to-end fusions with low support (remaining=2270)
[2026-06-08T09:25:54] Filtering fusions with no coverage around the breakpoints (remaining=2230)
[2026-06-08T09:25:55] Indexing gene sequences 
[2026-06-08T09:26:02] Filtering genes with >=30% identity (remaining=673)
[2026-06-08T09:26:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=258)
[2026-06-08T09:26:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=203)
[2026-06-08T09:26:12] Searching for additional isoforms (remaining=279)
[2026-06-08T09:26:14] Assigning confidence scores to events 
[2026-06-08T09:26:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:26:18] Writing fusions to file '659_ezg-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:26:21] Writing discarded fusions to file '659_ezg-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:26:59] Freeing resources
[2026-06-08T09:27:21] Done (elapsed time=00:13:26, CPU time=00:13:25, peak memory=17.1gb)