[2026-06-08T08:36:16] Launching Arriba 2.4.0
[2026-06-08T08:36:16] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:35] Reading chimeric alignments from '659_djb-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10409423)
[2026-06-08T08:44:16] Marking multi-mapping alignments (marked=6562302)
[2026-06-08T08:44:20] Detecting strandedness (reverse)
[2026-06-08T08:44:20] Assigning strands to alignments 
[2026-06-08T08:44:22] Annotating alignments 
[2026-06-08T08:44:55] Filtering duplicates (remaining=3553667)
[2026-06-08T08:45:00] 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=3375233)
[2026-06-08T08:45:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3375233)
[2026-06-08T08:45:04] Filtering viral contigs with expression lower than the top 5 (remaining=3375233)
[2026-06-08T08:45:08] Filtering viral contigs with less than 5% coverage (remaining=3375233)
[2026-06-08T08:45:10] Estimating fragment length (mate gap mean=-89.4459, mate gap stddev=27.0776, read length mean=130.596)
[2026-06-08T08:45:10] Filtering read-through fragments with a distance <=10000bp (remaining=3161697)
[2026-06-08T08:45:12] Filtering inconsistently clipped mates (remaining=3105778)
[2026-06-08T08:45:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2974305)
[2026-06-08T08:45:17] Filtering fragments with small insert size (remaining=2973631)
[2026-06-08T08:45:19] Filtering alignments with long gaps (remaining=2973631)
[2026-06-08T08:45:21] Filtering fragments with both mates in the same gene (remaining=2972988)
[2026-06-08T08:45:23] Filtering fusions arising from hairpin structures (remaining=2836640)
[2026-06-08T08:45:25] Filtering reads with a mismatch p-value <=0.01 (remaining=1181971)
[2026-06-08T08:45:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=545434)
[2026-06-08T08:45:41] Finding fusions and counting supporting reads (total=464630)
[2026-06-08T08:45:55] Merging adjacent fusion breakpoints (remaining=458611)
[2026-06-08T08:45:56] Filtering multi-mapping fusions by alignment score and read support (remaining=250932)
[2026-06-08T08:46:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=249549)
[2026-06-08T08:46:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=136372)
[2026-06-08T08:46:33] Filtering fusions with <2 supporting reads (remaining=15954)
[2026-06-08T08:46:34] Filtering fusions with an e-value >=0.3 (remaining=4170)
[2026-06-08T08:46:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4200)
[2026-06-08T08:46:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4133)
[2026-06-08T08:46:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4133)
[2026-06-08T08:46:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3997)
[2026-06-08T08:46:42] Searching for fusions with spliced split reads (remaining=4049)
[2026-06-08T08:46:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=2827)
[2026-06-08T08:46:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2799)
[2026-06-08T08:46:47] Searching for fusions with >=4 spliced events (remaining=3123)
[2026-06-08T08:46:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1085)
[2026-06-08T08:47:04] Filtering fusions with anchors <=23nt (remaining=945)
[2026-06-08T08:47:04] Filtering end-to-end fusions with low support (remaining=914)
[2026-06-08T08:47:04] Filtering fusions with no coverage around the breakpoints (remaining=887)
[2026-06-08T08:47:05] Indexing gene sequences 
[2026-06-08T08:47:09] Filtering genes with >=30% identity (remaining=285)
[2026-06-08T08:47:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=110)
[2026-06-08T08:47:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=108)
[2026-06-08T08:47:13] Searching for additional isoforms (remaining=134)
[2026-06-08T08:47:14] Assigning confidence scores to events 
[2026-06-08T08:47:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:16] Writing fusions to file '659_djb-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:18] Writing discarded fusions to file '659_djb-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:37] Freeing resources
[2026-06-08T08:47:54] Done (elapsed time=00:11:38, CPU time=00:11:36, peak memory=15gb)