[2026-06-08T08:25:10] Launching Arriba 2.4.0
[2026-06-08T08:25:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:24] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:29] Reading chimeric alignments from 'aih-tih-sc-5d3207-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=5616252)
[2026-06-08T08:30:12] Marking multi-mapping alignments (marked=3437287)
[2026-06-08T08:30:14] Detecting strandedness (reverse)
[2026-06-08T08:30:14] Assigning strands to alignments 
[2026-06-08T08:30:15] Annotating alignments 
[2026-06-08T08:30:33] Filtering duplicates (remaining=3639717)
[2026-06-08T08:30:36] 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=3501596)
[2026-06-08T08:30:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3501596)
[2026-06-08T08:30:38] Filtering viral contigs with expression lower than the top 5 (remaining=3501596)
[2026-06-08T08:30:41] Filtering viral contigs with less than 5% coverage (remaining=3501596)
[2026-06-08T08:30:42] Estimating fragment length (mate gap mean=-85.3995, mate gap stddev=30.0468, read length mean=134.46)
[2026-06-08T08:30:42] Filtering read-through fragments with a distance <=10000bp (remaining=3283530)
[2026-06-08T08:30:43] Filtering inconsistently clipped mates (remaining=3220346)
[2026-06-08T08:30:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3138346)
[2026-06-08T08:30:46] Filtering fragments with small insert size (remaining=3137892)
[2026-06-08T08:30:47] Filtering alignments with long gaps (remaining=3137892)
[2026-06-08T08:30:48] Filtering fragments with both mates in the same gene (remaining=3137191)
[2026-06-08T08:30:49] Filtering fusions arising from hairpin structures (remaining=2919493)
[2026-06-08T08:30:51] Filtering reads with a mismatch p-value <=0.01 (remaining=1452299)
[2026-06-08T08:30:58] Filtering reads with low entropy (k-mer content >=60%) (remaining=599813)
[2026-06-08T08:31:05] Finding fusions and counting supporting reads (total=454491)
[2026-06-08T08:31:13] Merging adjacent fusion breakpoints (remaining=451342)
[2026-06-08T08:31:14] Filtering multi-mapping fusions by alignment score and read support (remaining=295568)
[2026-06-08T08:31:33] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:31:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=293682)
[2026-06-08T08:31:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=153671)
[2026-06-08T08:31:38] Filtering fusions with <2 supporting reads (remaining=23644)
[2026-06-08T08:31:38] Filtering fusions with an e-value >=0.3 (remaining=7975)
[2026-06-08T08:31:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8020)
[2026-06-08T08:31:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7970)
[2026-06-08T08:31:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7970)
[2026-06-08T08:31:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5745)
[2026-06-08T08:31:44] Searching for fusions with spliced split reads (remaining=5835)
[2026-06-08T08:31:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=3578)
[2026-06-08T08:31:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3524)
[2026-06-08T08:31:49] Searching for fusions with >=4 spliced events (remaining=4016)
[2026-06-08T08:31:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1093)
[2026-06-08T08:32:08] Filtering fusions with anchors <=23nt (remaining=907)
[2026-06-08T08:32:08] Filtering end-to-end fusions with low support (remaining=885)
[2026-06-08T08:32:09] Filtering fusions with no coverage around the breakpoints (remaining=867)
[2026-06-08T08:32:09] Indexing gene sequences 
[2026-06-08T08:32:14] Filtering genes with >=30% identity (remaining=288)
[2026-06-08T08:32:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=163)
[2026-06-08T08:32:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=160)
[2026-06-08T08:32:22] Searching for additional isoforms (remaining=191)
[2026-06-08T08:32:23] Assigning confidence scores to events 
[2026-06-08T08:32:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:25] Writing fusions to file 'aih-tih-sc-5d3207-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:32:27] Writing discarded fusions to file 'aih-tih-sc-5d3207-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:32:47] Freeing resources
[2026-06-08T08:32:57] Done (elapsed time=00:07:47, CPU time=00:07:46, peak memory=10gb)