[2026-06-08T08:46:55] Launching Arriba 2.4.0
[2026-06-08T08:46:55] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:09] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:14] Reading chimeric alignments from 'aih-tih-sc-965752-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10538094)
[2026-06-08T08:55:19] Marking multi-mapping alignments (marked=6778324)
[2026-06-08T08:55:24] Detecting strandedness (reverse)
[2026-06-08T08:55:24] Assigning strands to alignments 
[2026-06-08T08:55:26] Annotating alignments 
[2026-06-08T08:56:04] Filtering duplicates (remaining=5996970)
[2026-06-08T08:56:12] 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=5730943)
[2026-06-08T08:56:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5730943)
[2026-06-08T08:56:16] Filtering viral contigs with expression lower than the top 5 (remaining=5730943)
[2026-06-08T08:56:21] Filtering viral contigs with less than 5% coverage (remaining=5730943)
[2026-06-08T08:56:24] Estimating fragment length (mate gap mean=-86.3144, mate gap stddev=27.8725, read length mean=126.051)
[2026-06-08T08:56:24] Filtering read-through fragments with a distance <=10000bp (remaining=5339486)
[2026-06-08T08:56:26] Filtering inconsistently clipped mates (remaining=5234931)
[2026-06-08T08:56:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5118161)
[2026-06-08T08:56:34] Filtering fragments with small insert size (remaining=5116897)
[2026-06-08T08:56:36] Filtering alignments with long gaps (remaining=5116897)
[2026-06-08T08:56:38] Filtering fragments with both mates in the same gene (remaining=5115954)
[2026-06-08T08:56:41] Filtering fusions arising from hairpin structures (remaining=4813546)
[2026-06-08T08:56:44] Filtering reads with a mismatch p-value <=0.01 (remaining=2010399)
[2026-06-08T08:56:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=870672)
[2026-06-08T08:57:07] Finding fusions and counting supporting reads (total=698300)
[2026-06-08T08:57:26] Merging adjacent fusion breakpoints (remaining=688780)
[2026-06-08T08:57:28] Filtering multi-mapping fusions by alignment score and read support (remaining=429890)
[2026-06-08T08:58:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=428273)
[2026-06-08T08:58:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=235710)
[2026-06-08T08:58:14] Filtering fusions with <2 supporting reads (remaining=27588)
[2026-06-08T08:58:15] Filtering fusions with an e-value >=0.3 (remaining=6597)
[2026-06-08T08:58:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6652)
[2026-06-08T08:58:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6568)
[2026-06-08T08:58:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6572)
[2026-06-08T08:58:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5838)
[2026-06-08T08:58:26] Searching for fusions with spliced split reads (remaining=5958)
[2026-06-08T08:58:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=3821)
[2026-06-08T08:58:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3767)
[2026-06-08T08:58:34] Searching for fusions with >=4 spliced events (remaining=4601)
[2026-06-08T08:58:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2094)
[2026-06-08T08:58:50] Filtering fusions with anchors <=23nt (remaining=1753)
[2026-06-08T08:58:50] Filtering end-to-end fusions with low support (remaining=1715)
[2026-06-08T08:58:51] Filtering fusions with no coverage around the breakpoints (remaining=1691)
[2026-06-08T08:58:52] Indexing gene sequences 
[2026-06-08T08:58:58] Filtering genes with >=30% identity (remaining=546)
[2026-06-08T08:59:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=225)
[2026-06-08T08:59:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=202)
[2026-06-08T08:59:07] Searching for additional isoforms (remaining=278)
[2026-06-08T08:59:08] Assigning confidence scores to events 
[2026-06-08T08:59:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:12] Writing fusions to file 'aih-tih-sc-965752-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:14] Writing discarded fusions to file 'aih-tih-sc-965752-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:47] Freeing resources
[2026-06-08T09:00:06] Done (elapsed time=00:13:11, CPU time=00:13:09, peak memory=15.2gb)