[2026-06-08T08:16:07] Launching Arriba 2.4.0
[2026-06-08T08:16:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:16:20] Reading chimeric alignments from 'aih-tih-sc-790e56-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=6221485)
[2026-06-08T08:20:40] Marking multi-mapping alignments (marked=4111656)
[2026-06-08T08:20:43] Detecting strandedness (reverse)
[2026-06-08T08:20:43] Assigning strands to alignments 
[2026-06-08T08:20:45] Annotating alignments 
[2026-06-08T08:21:18] Filtering duplicates (remaining=4495730)
[2026-06-08T08:21:24] 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=4227022)
[2026-06-08T08:21:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4227022)
[2026-06-08T08:21:28] Filtering viral contigs with expression lower than the top 5 (remaining=4227022)
[2026-06-08T08:21:32] Filtering viral contigs with less than 5% coverage (remaining=4227022)
[2026-06-08T08:21:34] Estimating fragment length (mate gap mean=-85.4544, mate gap stddev=29.3686, read length mean=128.164)
[2026-06-08T08:21:34] Filtering read-through fragments with a distance <=10000bp (remaining=3973717)
[2026-06-08T08:21:36] Filtering inconsistently clipped mates (remaining=3885339)
[2026-06-08T08:21:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3766998)
[2026-06-08T08:21:42] Filtering fragments with small insert size (remaining=3766391)
[2026-06-08T08:21:44] Filtering alignments with long gaps (remaining=3766391)
[2026-06-08T08:21:46] Filtering fragments with both mates in the same gene (remaining=3765568)
[2026-06-08T08:21:48] Filtering fusions arising from hairpin structures (remaining=3494746)
[2026-06-08T08:21:50] Filtering reads with a mismatch p-value <=0.01 (remaining=1520257)
[2026-06-08T08:22:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=744865)
[2026-06-08T08:22:09] Finding fusions and counting supporting reads (total=609254)
[2026-06-08T08:22:27] Merging adjacent fusion breakpoints (remaining=603883)
[2026-06-08T08:22:29] Filtering multi-mapping fusions by alignment score and read support (remaining=367725)
[2026-06-08T08:22:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:23:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=366034)
[2026-06-08T08:23:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=224995)
[2026-06-08T08:23:07] Filtering fusions with <2 supporting reads (remaining=26811)
[2026-06-08T08:23:08] Filtering fusions with an e-value >=0.3 (remaining=9385)
[2026-06-08T08:23:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9448)
[2026-06-08T08:23:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9406)
[2026-06-08T08:23:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9406)
[2026-06-08T08:23:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4787)
[2026-06-08T08:23:20] Searching for fusions with spliced split reads (remaining=4889)
[2026-06-08T08:23:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=3307)
[2026-06-08T08:23:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3250)
[2026-06-08T08:23:27] Searching for fusions with >=4 spliced events (remaining=3770)
[2026-06-08T08:23:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1415)
[2026-06-08T08:23:48] Filtering fusions with anchors <=23nt (remaining=1096)
[2026-06-08T08:23:49] Filtering end-to-end fusions with low support (remaining=1060)
[2026-06-08T08:23:50] Filtering fusions with no coverage around the breakpoints (remaining=1032)
[2026-06-08T08:23:51] Indexing gene sequences 
[2026-06-08T08:23:58] Filtering genes with >=30% identity (remaining=361)
[2026-06-08T08:24:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=218)
[2026-06-08T08:24:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=179)
[2026-06-08T08:24:06] Searching for additional isoforms (remaining=211)
[2026-06-08T08:24:08] Assigning confidence scores to events 
[2026-06-08T08:24:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:24:12] Writing fusions to file 'aih-tih-sc-790e56-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:24:15] Writing discarded fusions to file 'aih-tih-sc-790e56-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:24:51] Freeing resources
[2026-06-08T08:25:07] Done (elapsed time=00:09:00, CPU time=00:08:58, peak memory=10.8gb)