[2026-06-08T08:24:58] Launching Arriba 2.4.0
[2026-06-08T08:24:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:07] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:10] Reading chimeric alignments from 'aih-tih-sc-2ca847-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=6601804)
[2026-06-08T08:28:49] Marking multi-mapping alignments (marked=4404262)
[2026-06-08T08:28:51] Detecting strandedness (reverse)
[2026-06-08T08:28:51] Assigning strands to alignments 
[2026-06-08T08:28:53] Annotating alignments 
[2026-06-08T08:29:13] Filtering duplicates (remaining=2782507)
[2026-06-08T08:29:16] 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=2564873)
[2026-06-08T08:29:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2564873)
[2026-06-08T08:29:19] Filtering viral contigs with expression lower than the top 5 (remaining=2564873)
[2026-06-08T08:29:21] Filtering viral contigs with less than 5% coverage (remaining=2564873)
[2026-06-08T08:29:22] Estimating fragment length (mate gap mean=-84.7963, mate gap stddev=27.7153, read length mean=122.763)
[2026-06-08T08:29:23] Filtering read-through fragments with a distance <=10000bp (remaining=2420810)
[2026-06-08T08:29:24] Filtering inconsistently clipped mates (remaining=2361821)
[2026-06-08T08:29:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2301781)
[2026-06-08T08:29:27] Filtering fragments with small insert size (remaining=2301091)
[2026-06-08T08:29:28] Filtering alignments with long gaps (remaining=2301091)
[2026-06-08T08:29:29] Filtering fragments with both mates in the same gene (remaining=2300619)
[2026-06-08T08:29:30] Filtering fusions arising from hairpin structures (remaining=2145774)
[2026-06-08T08:29:32] Filtering reads with a mismatch p-value <=0.01 (remaining=927746)
[2026-06-08T08:29:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=354642)
[2026-06-08T08:29:42] Finding fusions and counting supporting reads (total=303575)
[2026-06-08T08:29:51] Merging adjacent fusion breakpoints (remaining=300758)
[2026-06-08T08:29:51] Filtering multi-mapping fusions by alignment score and read support (remaining=173672)
[2026-06-08T08:30:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:30:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=172658)
[2026-06-08T08:30:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=97358)
[2026-06-08T08:30:14] Filtering fusions with <2 supporting reads (remaining=9825)
[2026-06-08T08:30:15] Filtering fusions with an e-value >=0.3 (remaining=2515)
[2026-06-08T08:30:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2555)
[2026-06-08T08:30:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2523)
[2026-06-08T08:30:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2523)
[2026-06-08T08:30:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2267)
[2026-06-08T08:30:21] Searching for fusions with spliced split reads (remaining=2319)
[2026-06-08T08:30:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=1726)
[2026-06-08T08:30:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1696)
[2026-06-08T08:30:24] Searching for fusions with >=4 spliced events (remaining=1928)
[2026-06-08T08:30:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=731)
[2026-06-08T08:30:36] Filtering fusions with anchors <=23nt (remaining=636)
[2026-06-08T08:30:37] Filtering end-to-end fusions with low support (remaining=611)
[2026-06-08T08:30:37] Filtering fusions with no coverage around the breakpoints (remaining=599)
[2026-06-08T08:30:37] Indexing gene sequences 
[2026-06-08T08:30:40] Filtering genes with >=30% identity (remaining=231)
[2026-06-08T08:30:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=129)
[2026-06-08T08:30:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=113)
[2026-06-08T08:30:43] Searching for additional isoforms (remaining=139)
[2026-06-08T08:30:44] Assigning confidence scores to events 
[2026-06-08T08:30:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:45] Writing fusions to file 'aih-tih-sc-2ca847-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:30:46] Writing discarded fusions to file 'aih-tih-sc-2ca847-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:30:58] Freeing resources
[2026-06-08T08:31:08] Done (elapsed time=00:06:10, CPU time=00:06:09, peak memory=10.9gb)