[2026-06-08T09:03:36] Launching Arriba 2.4.0
[2026-06-08T09:03:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:03:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:03:49] Reading chimeric alignments from '659_dc8-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=11846372)
[2026-06-08T09:11:07] Marking multi-mapping alignments (marked=7156048)
[2026-06-08T09:11:12] Detecting strandedness (reverse)
[2026-06-08T09:11:12] Assigning strands to alignments 
[2026-06-08T09:11:15] Annotating alignments 
[2026-06-08T09:11:59] Filtering duplicates (remaining=7282312)
[2026-06-08T09:12:09] 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=7067602)
[2026-06-08T09:12:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7067602)
[2026-06-08T09:12:15] Filtering viral contigs with expression lower than the top 5 (remaining=7067602)
[2026-06-08T09:12:21] Filtering viral contigs with less than 5% coverage (remaining=7067602)
[2026-06-08T09:12:24] Estimating fragment length (mate gap mean=-89.0304, mate gap stddev=29.4988, read length mean=138.918)
[2026-06-08T09:12:25] Filtering read-through fragments with a distance <=10000bp (remaining=6615312)
[2026-06-08T09:12:28] Filtering inconsistently clipped mates (remaining=6520504)
[2026-06-08T09:12:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6338529)
[2026-06-08T09:12:36] Filtering fragments with small insert size (remaining=6337830)
[2026-06-08T09:12:39] Filtering alignments with long gaps (remaining=6337830)
[2026-06-08T09:12:41] Filtering fragments with both mates in the same gene (remaining=6336853)
[2026-06-08T09:12:44] Filtering fusions arising from hairpin structures (remaining=5973982)
[2026-06-08T09:12:47] Filtering reads with a mismatch p-value <=0.01 (remaining=3152358)
[2026-06-08T09:13:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=1153558)
[2026-06-08T09:13:18] Finding fusions and counting supporting reads (total=881593)
[2026-06-08T09:13:40] Merging adjacent fusion breakpoints (remaining=871768)
[2026-06-08T09:13:42] Filtering multi-mapping fusions by alignment score and read support (remaining=548670)
[2026-06-08T09:14:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:14:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=544611)
[2026-06-08T09:14:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=289736)
[2026-06-08T09:14:36] Filtering fusions with <2 supporting reads (remaining=44923)
[2026-06-08T09:14:36] Filtering fusions with an e-value >=0.3 (remaining=14831)
[2026-06-08T09:14:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14886)
[2026-06-08T09:14:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14753)
[2026-06-08T09:14:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14768)
[2026-06-08T09:14:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9689)
[2026-06-08T09:14:51] Searching for fusions with spliced split reads (remaining=9710)
[2026-06-08T09:14:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=5465)
[2026-06-08T09:14:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5411)
[2026-06-08T09:15:00] Searching for fusions with >=4 spliced events (remaining=6590)
[2026-06-08T09:15:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2328)
[2026-06-08T09:15:19] Filtering fusions with anchors <=23nt (remaining=1853)
[2026-06-08T09:15:20] Filtering end-to-end fusions with low support (remaining=1808)
[2026-06-08T09:15:21] Filtering fusions with no coverage around the breakpoints (remaining=1753)
[2026-06-08T09:15:22] Indexing gene sequences 
[2026-06-08T09:15:28] Filtering genes with >=30% identity (remaining=470)
[2026-06-08T09:15:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=190)
[2026-06-08T09:15:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=162)
[2026-06-08T09:15:40] Searching for additional isoforms (remaining=233)
[2026-06-08T09:15:42] Assigning confidence scores to events 
[2026-06-08T09:15:46] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:15:46] Writing fusions to file '659_dc8-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:15:48] Writing discarded fusions to file '659_dc8-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:16:26] Freeing resources
[2026-06-08T09:16:48] Done (elapsed time=00:13:12, CPU time=00:13:11, peak memory=16.4gb)