[2026-06-08T08:40:23] Launching Arriba 2.4.0
[2026-06-08T08:40:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:38] Reading chimeric alignments from '659_ecd-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=8880761)
[2026-06-08T08:45:57] Marking multi-mapping alignments (marked=5283298)
[2026-06-08T08:46:00] Detecting strandedness (reverse)
[2026-06-08T08:46:00] Assigning strands to alignments 
[2026-06-08T08:46:02] Annotating alignments 
[2026-06-08T08:46:27] Filtering duplicates (remaining=6046479)
[2026-06-08T08:46:33] 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=5925722)
[2026-06-08T08:46:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5925722)
[2026-06-08T08:46:36] Filtering viral contigs with expression lower than the top 5 (remaining=5925722)
[2026-06-08T08:46:39] Filtering viral contigs with less than 5% coverage (remaining=5925722)
[2026-06-08T08:46:41] Estimating fragment length (mate gap mean=-86.0789, mate gap stddev=33.0707, read length mean=142.786)
[2026-06-08T08:46:41] Filtering read-through fragments with a distance <=10000bp (remaining=5583232)
[2026-06-08T08:46:43] Filtering inconsistently clipped mates (remaining=5524272)
[2026-06-08T08:46:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5331976)
[2026-06-08T08:46:47] Filtering fragments with small insert size (remaining=5331638)
[2026-06-08T08:46:48] Filtering alignments with long gaps (remaining=5331637)
[2026-06-08T08:46:50] Filtering fragments with both mates in the same gene (remaining=5330484)
[2026-06-08T08:46:51] Filtering fusions arising from hairpin structures (remaining=5070065)
[2026-06-08T08:46:53] Filtering reads with a mismatch p-value <=0.01 (remaining=2738224)
[2026-06-08T08:47:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=964321)
[2026-06-08T08:47:15] Finding fusions and counting supporting reads (total=705195)
[2026-06-08T08:47:27] Merging adjacent fusion breakpoints (remaining=701101)
[2026-06-08T08:47:29] Filtering multi-mapping fusions by alignment score and read support (remaining=466061)
[2026-06-08T08:47:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=462630)
[2026-06-08T08:47:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=246510)
[2026-06-08T08:47:59] Filtering fusions with <2 supporting reads (remaining=43401)
[2026-06-08T08:48:00] Filtering fusions with an e-value >=0.3 (remaining=16978)
[2026-06-08T08:48:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17030)
[2026-06-08T08:48:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16942)
[2026-06-08T08:48:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=16968)
[2026-06-08T08:48:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9966)
[2026-06-08T08:48:09] Searching for fusions with spliced split reads (remaining=10041)
[2026-06-08T08:48:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=4937)
[2026-06-08T08:48:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4883)
[2026-06-08T08:48:15] Searching for fusions with >=4 spliced events (remaining=5930)
[2026-06-08T08:48:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2165)
[2026-06-08T08:48:29] Filtering fusions with anchors <=23nt (remaining=1829)
[2026-06-08T08:48:29] Filtering end-to-end fusions with low support (remaining=1781)
[2026-06-08T08:48:30] Filtering fusions with no coverage around the breakpoints (remaining=1737)
[2026-06-08T08:48:31] Indexing gene sequences 
[2026-06-08T08:48:38] Filtering genes with >=30% identity (remaining=662)
[2026-06-08T08:48:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=453)
[2026-06-08T08:48:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=343)
[2026-06-08T08:48:50] Searching for additional isoforms (remaining=533)
[2026-06-08T08:48:51] Assigning confidence scores to events 
[2026-06-08T08:48:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:54] Writing fusions to file '659_ecd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T08:48:58] Writing discarded fusions to file '659_ecd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:49:21] Freeing resources
[2026-06-08T08:49:36] Done (elapsed time=00:09:13, CPU time=00:09:12, peak memory=13.4gb)