[2026-06-08T08:58:21] Launching Arriba 2.4.0
[2026-06-08T08:58:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:58:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:34] Reading chimeric alignments from 'aih-tih-sc-4ca6a8-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10520902)
[2026-06-08T09:05:59] Marking multi-mapping alignments (marked=6421651)
[2026-06-08T09:06:03] Detecting strandedness (reverse)
[2026-06-08T09:06:03] Assigning strands to alignments 
[2026-06-08T09:06:05] Annotating alignments 
[2026-06-08T09:06:41] Filtering duplicates (remaining=6079800)
[2026-06-08T09:06:49] 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=5765261)
[2026-06-08T09:06:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5765261)
[2026-06-08T09:06:53] Filtering viral contigs with expression lower than the top 5 (remaining=5765261)
[2026-06-08T09:06:58] Filtering viral contigs with less than 5% coverage (remaining=5765261)
[2026-06-08T09:07:01] Estimating fragment length (mate gap mean=-87.5152, mate gap stddev=28.5343, read length mean=132.248)
[2026-06-08T09:07:01] Filtering read-through fragments with a distance <=10000bp (remaining=5351859)
[2026-06-08T09:07:03] Filtering inconsistently clipped mates (remaining=5253276)
[2026-06-08T09:07:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5142866)
[2026-06-08T09:07:10] Filtering fragments with small insert size (remaining=5141496)
[2026-06-08T09:07:12] Filtering alignments with long gaps (remaining=5141495)
[2026-06-08T09:07:15] Filtering fragments with both mates in the same gene (remaining=5140474)
[2026-06-08T09:07:17] Filtering fusions arising from hairpin structures (remaining=4830030)
[2026-06-08T09:07:20] Filtering reads with a mismatch p-value <=0.01 (remaining=2211737)
[2026-06-08T09:07:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=1041283)
[2026-06-08T09:07:43] Finding fusions and counting supporting reads (total=749672)
[2026-06-08T09:08:01] Merging adjacent fusion breakpoints (remaining=741387)
[2026-06-08T09:08:02] Filtering multi-mapping fusions by alignment score and read support (remaining=480487)
[2026-06-08T09:08:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:08:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=478505)
[2026-06-08T09:08:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=247625)
[2026-06-08T09:08:44] Filtering fusions with <2 supporting reads (remaining=37112)
[2026-06-08T09:08:45] Filtering fusions with an e-value >=0.3 (remaining=10065)
[2026-06-08T09:08:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10145)
[2026-06-08T09:08:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10079)
[2026-06-08T09:08:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10079)
[2026-06-08T09:08:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7656)
[2026-06-08T09:08:56] Searching for fusions with spliced split reads (remaining=7777)
[2026-06-08T09:09:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=4780)
[2026-06-08T09:09:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4724)
[2026-06-08T09:09:03] Searching for fusions with >=4 spliced events (remaining=5738)
[2026-06-08T09:09:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2161)
[2026-06-08T09:09:19] Filtering fusions with anchors <=23nt (remaining=1821)
[2026-06-08T09:09:19] Filtering end-to-end fusions with low support (remaining=1759)
[2026-06-08T09:09:20] Filtering fusions with no coverage around the breakpoints (remaining=1723)
[2026-06-08T09:09:21] Indexing gene sequences 
[2026-06-08T09:09:27] Filtering genes with >=30% identity (remaining=571)
[2026-06-08T09:09:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=322)
[2026-06-08T09:09:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=257)
[2026-06-08T09:09:38] Searching for additional isoforms (remaining=333)
[2026-06-08T09:09:39] Assigning confidence scores to events 
[2026-06-08T09:09:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:42] Writing fusions to file 'aih-tih-sc-4ca6a8-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:09:45] Writing discarded fusions to file 'aih-tih-sc-4ca6a8-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:15] Freeing resources
[2026-06-08T09:10:32] Done (elapsed time=00:12:11, CPU time=00:12:10, peak memory=15.3gb)