[2026-06-08T08:07:24] Launching Arriba 2.4.0
[2026-06-08T08:07:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:07:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:07:43] Reading chimeric alignments from 'aih-tih-sc-8e3550-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=5582380)
[2026-06-08T08:11:41] Marking multi-mapping alignments (marked=3712244)
[2026-06-08T08:11:43] Detecting strandedness (reverse)
[2026-06-08T08:11:43] Assigning strands to alignments 
[2026-06-08T08:11:44] Annotating alignments 
[2026-06-08T08:12:01] Filtering duplicates (remaining=4045206)
[2026-06-08T08:12:04] 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=3822895)
[2026-06-08T08:12:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3822895)
[2026-06-08T08:12:06] Filtering viral contigs with expression lower than the top 5 (remaining=3822895)
[2026-06-08T08:12:09] Filtering viral contigs with less than 5% coverage (remaining=3822895)
[2026-06-08T08:12:10] Estimating fragment length (mate gap mean=-83.9201, mate gap stddev=30.7027, read length mean=132.036)
[2026-06-08T08:12:10] Filtering read-through fragments with a distance <=10000bp (remaining=3626114)
[2026-06-08T08:12:11] Filtering inconsistently clipped mates (remaining=3554722)
[2026-06-08T08:12:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3459465)
[2026-06-08T08:12:14] Filtering fragments with small insert size (remaining=3458949)
[2026-06-08T08:12:15] Filtering alignments with long gaps (remaining=3458949)
[2026-06-08T08:12:16] Filtering fragments with both mates in the same gene (remaining=3458266)
[2026-06-08T08:12:17] Filtering fusions arising from hairpin structures (remaining=3208671)
[2026-06-08T08:12:19] Filtering reads with a mismatch p-value <=0.01 (remaining=1522249)
[2026-06-08T08:12:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=690035)
[2026-06-08T08:12:32] Finding fusions and counting supporting reads (total=558816)
[2026-06-08T08:12:41] Merging adjacent fusion breakpoints (remaining=555506)
[2026-06-08T08:12:42] Filtering multi-mapping fusions by alignment score and read support (remaining=342526)
[2026-06-08T08:12:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:13:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=340801)
[2026-06-08T08:13:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=210429)
[2026-06-08T08:13:02] Filtering fusions with <2 supporting reads (remaining=22597)
[2026-06-08T08:13:02] Filtering fusions with an e-value >=0.3 (remaining=7984)
[2026-06-08T08:13:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8031)
[2026-06-08T08:13:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7956)
[2026-06-08T08:13:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7956)
[2026-06-08T08:13:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5361)
[2026-06-08T08:13:09] Searching for fusions with spliced split reads (remaining=5467)
[2026-06-08T08:13:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=3010)
[2026-06-08T08:13:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2971)
[2026-06-08T08:13:13] Searching for fusions with >=4 spliced events (remaining=3625)
[2026-06-08T08:13:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1571)
[2026-06-08T08:13:28] Filtering fusions with anchors <=23nt (remaining=1322)
[2026-06-08T08:13:28] Filtering end-to-end fusions with low support (remaining=1299)
[2026-06-08T08:13:29] Filtering fusions with no coverage around the breakpoints (remaining=1273)
[2026-06-08T08:13:29] Indexing gene sequences 
[2026-06-08T08:13:35] Filtering genes with >=30% identity (remaining=564)
[2026-06-08T08:13:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=390)
[2026-06-08T08:13:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=271)
[2026-06-08T08:13:42] Searching for additional isoforms (remaining=367)
[2026-06-08T08:13:43] Assigning confidence scores to events 
[2026-06-08T08:13:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:13:45] Writing fusions to file 'aih-tih-sc-8e3550-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:13:48] Writing discarded fusions to file 'aih-tih-sc-8e3550-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:14:06] Freeing resources
[2026-06-08T08:14:16] Done (elapsed time=00:06:52, CPU time=00:06:51, peak memory=10.1gb)