[2026-06-08T09:02:37] Launching Arriba 2.4.0
[2026-06-08T09:02:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:02:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:02:49] Reading chimeric alignments from 'PX_FFPE_bld_TRNA_nat_01_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=12307109)
[2026-06-08T09:09:53] Marking multi-mapping alignments (marked=7302930)
[2026-06-08T09:09:58] Detecting strandedness (reverse)
[2026-06-08T09:09:58] Assigning strands to alignments 
[2026-06-08T09:10:01] Annotating alignments 
[2026-06-08T09:10:43] Filtering duplicates (remaining=7506422)
[2026-06-08T09:10:52] 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=7288699)
[2026-06-08T09:10:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7288699)
[2026-06-08T09:10:57] Filtering viral contigs with expression lower than the top 5 (remaining=7288699)
[2026-06-08T09:11:02] Filtering viral contigs with less than 5% coverage (remaining=7288699)
[2026-06-08T09:11:05] Estimating fragment length (mate gap mean=-89.2973, mate gap stddev=27.6245, read length mean=133.68)
[2026-06-08T09:11:05] Filtering read-through fragments with a distance <=10000bp (remaining=6747897)
[2026-06-08T09:11:08] Filtering inconsistently clipped mates (remaining=6643700)
[2026-06-08T09:11:10] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6491979)
[2026-06-08T09:11:15] Filtering fragments with small insert size (remaining=6491043)
[2026-06-08T09:11:18] Filtering alignments with long gaps (remaining=6491043)
[2026-06-08T09:11:20] Filtering fragments with both mates in the same gene (remaining=6490111)
[2026-06-08T09:11:23] Filtering fusions arising from hairpin structures (remaining=6132480)
[2026-06-08T09:11:26] Filtering reads with a mismatch p-value <=0.01 (remaining=3163907)
[2026-06-08T09:11:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=1405416)
[2026-06-08T09:11:56] Finding fusions and counting supporting reads (total=1006758)
[2026-06-08T09:12:16] Merging adjacent fusion breakpoints (remaining=996507)
[2026-06-08T09:12:18] Filtering multi-mapping fusions by alignment score and read support (remaining=634692)
[2026-06-08T09:12:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:13:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=631093)
[2026-06-08T09:13:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=335792)
[2026-06-08T09:13:09] Filtering fusions with <2 supporting reads (remaining=46433)
[2026-06-08T09:13:10] Filtering fusions with an e-value >=0.3 (remaining=10884)
[2026-06-08T09:13:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10935)
[2026-06-08T09:13:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10834)
[2026-06-08T09:13:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10834)
[2026-06-08T09:13:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9528)
[2026-06-08T09:13:24] Searching for fusions with spliced split reads (remaining=9543)
[2026-06-08T09:13:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=5729)
[2026-06-08T09:13:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5670)
[2026-06-08T09:13:33] Searching for fusions with >=4 spliced events (remaining=7169)
[2026-06-08T09:13:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2578)
[2026-06-08T09:13:48] Filtering fusions with anchors <=23nt (remaining=2209)
[2026-06-08T09:13:49] Filtering end-to-end fusions with low support (remaining=2152)
[2026-06-08T09:13:50] Filtering fusions with no coverage around the breakpoints (remaining=2110)
[2026-06-08T09:13:51] Indexing gene sequences 
[2026-06-08T09:13:57] Filtering genes with >=30% identity (remaining=562)
[2026-06-08T09:14:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=184)
[2026-06-08T09:14:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=160)
[2026-06-08T09:14:06] Searching for additional isoforms (remaining=216)
[2026-06-08T09:14:08] Assigning confidence scores to events 
[2026-06-08T09:14:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:14:12] Writing fusions to file 'PX_FFPE_bld_TRNA_nat_01_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:14:14] Writing discarded fusions to file 'PX_FFPE_bld_TRNA_nat_01_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:14:49] Freeing resources
[2026-06-08T09:15:10] Done (elapsed time=00:12:33, CPU time=00:12:32, peak memory=17gb)