[2026-06-03T20:10:50] Launching Arriba 2.4.0
[2026-06-03T20:10:50] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:10:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:11:03] Reading chimeric alignments from 'aih-tih-sc-5519ab-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11136481)
[2026-06-03T20:18:42] Marking multi-mapping alignments (marked=7779384)
[2026-06-03T20:18:47] Detecting strandedness (no)
[2026-06-03T20:18:47] Annotating alignments 
[2026-06-03T20:19:34] Filtering duplicates (remaining=6187890)
[2026-06-03T20:19:43] 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=5586948)
[2026-06-03T20:19:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5586948)
[2026-06-03T20:19:48] Filtering viral contigs with expression lower than the top 5 (remaining=5586948)
[2026-06-03T20:19:53] Filtering viral contigs with less than 5% coverage (remaining=5586948)
[2026-06-03T20:19:56] Estimating fragment length (mate gap mean=-82.7543, mate gap stddev=29.5925, read length mean=122.557)
[2026-06-03T20:19:56] Filtering read-through fragments with a distance <=10000bp (remaining=5342915)
[2026-06-03T20:19:59] Filtering inconsistently clipped mates (remaining=5200167)
[2026-06-03T20:20:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5030825)
[2026-06-03T20:20:07] Filtering fragments with small insert size (remaining=5029561)
[2026-06-03T20:20:09] Filtering alignments with long gaps (remaining=5029559)
[2026-06-03T20:20:12] Filtering fragments with both mates in the same gene (remaining=5028237)
[2026-06-03T20:20:15] Filtering fusions arising from hairpin structures (remaining=4629312)
[2026-06-03T20:20:18] Filtering reads with a mismatch p-value <=0.01 (remaining=1858347)
[2026-06-03T20:20:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=838757)
[2026-06-03T20:20:42] Finding fusions and counting supporting reads (total=655976)
[2026-06-03T20:21:00] Merging adjacent fusion breakpoints (remaining=648152)
[2026-06-03T20:21:01] Filtering multi-mapping fusions by alignment score and read support (remaining=384215)
[2026-06-03T20:21:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:21:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=381922)
[2026-06-03T20:21:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=236631)
[2026-06-03T20:21:50] Filtering fusions with <2 supporting reads (remaining=25678)
[2026-06-03T20:21:50] Filtering fusions with an e-value >=0.3 (remaining=6126)
[2026-06-03T20:21:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6182)
[2026-06-03T20:21:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6054)
[2026-06-03T20:21:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6054)
[2026-06-03T20:21:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5652)
[2026-06-03T20:22:03] Searching for fusions with spliced split reads (remaining=5785)
[2026-06-03T20:22:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=3817)
[2026-06-03T20:22:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3770)
[2026-06-03T20:22:11] Searching for fusions with >=4 spliced events (remaining=4433)
[2026-06-03T20:22:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1681)
[2026-06-03T20:22:27] Filtering fusions with anchors <=23nt (remaining=1393)
[2026-06-03T20:22:28] Filtering end-to-end fusions with low support (remaining=1348)
[2026-06-03T20:22:29] Filtering fusions with no coverage around the breakpoints (remaining=1329)
[2026-06-03T20:22:29] Indexing gene sequences 
[2026-06-03T20:22:36] Filtering genes with >=30% identity (remaining=504)
[2026-06-03T20:22:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=261)
[2026-06-03T20:22:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=239)
[2026-06-03T20:22:45] Searching for additional isoforms (remaining=315)
[2026-06-03T20:22:47] Assigning confidence scores to events 
[2026-06-03T20:22:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:22:51] Writing fusions to file 'aih-tih-sc-5519ab-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:22:54] Writing discarded fusions to file 'aih-tih-sc-5519ab-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:23:25] Freeing resources
[2026-06-03T20:23:43] Done (elapsed time=00:12:53, CPU time=00:12:53, peak memory=15.9gb)