[2026-06-08T08:19:17] Launching Arriba 2.4.0
[2026-06-08T08:19:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:25] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:30] Reading chimeric alignments from 'aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7576450)
[2026-06-08T08:24:36] Marking multi-mapping alignments (marked=4911825)
[2026-06-08T08:24:39] Detecting strandedness (reverse)
[2026-06-08T08:24:39] Assigning strands to alignments 
[2026-06-08T08:24:41] Annotating alignments 
[2026-06-08T08:25:06] Filtering duplicates (remaining=5447051)
[2026-06-08T08:25:12] 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=5163577)
[2026-06-08T08:25:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5163577)
[2026-06-08T08:25:15] Filtering viral contigs with expression lower than the top 5 (remaining=5163577)
[2026-06-08T08:25:18] Filtering viral contigs with less than 5% coverage (remaining=5163577)
[2026-06-08T08:25:20] Estimating fragment length (mate gap mean=-85.4998, mate gap stddev=28.5952, read length mean=129.501)
[2026-06-08T08:25:20] Filtering read-through fragments with a distance <=10000bp (remaining=4868644)
[2026-06-08T08:25:22] Filtering inconsistently clipped mates (remaining=4769796)
[2026-06-08T08:25:23] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4640929)
[2026-06-08T08:25:27] Filtering fragments with small insert size (remaining=4640179)
[2026-06-08T08:25:28] Filtering alignments with long gaps (remaining=4640179)
[2026-06-08T08:25:30] Filtering fragments with both mates in the same gene (remaining=4639291)
[2026-06-08T08:25:32] Filtering fusions arising from hairpin structures (remaining=4317554)
[2026-06-08T08:25:34] Filtering reads with a mismatch p-value <=0.01 (remaining=1975865)
[2026-06-08T08:25:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=929020)
[2026-06-08T08:25:56] Finding fusions and counting supporting reads (total=741437)
[2026-06-08T08:26:09] Merging adjacent fusion breakpoints (remaining=736762)
[2026-06-08T08:26:10] Filtering multi-mapping fusions by alignment score and read support (remaining=466297)
[2026-06-08T08:26:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:26:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=464703)
[2026-06-08T08:26:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=295288)
[2026-06-08T08:26:43] Filtering fusions with <2 supporting reads (remaining=27919)
[2026-06-08T08:26:43] Filtering fusions with an e-value >=0.3 (remaining=6546)
[2026-06-08T08:26:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6603)
[2026-06-08T08:26:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6552)
[2026-06-08T08:26:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6552)
[2026-06-08T08:26:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5853)
[2026-06-08T08:26:53] Searching for fusions with spliced split reads (remaining=5969)
[2026-06-08T08:26:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=3879)
[2026-06-08T08:26:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3829)
[2026-06-08T08:26:59] Searching for fusions with >=4 spliced events (remaining=4617)
[2026-06-08T08:27:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1738)
[2026-06-08T08:27:13] Filtering fusions with anchors <=23nt (remaining=1409)
[2026-06-08T08:27:14] Filtering end-to-end fusions with low support (remaining=1367)
[2026-06-08T08:27:14] Filtering fusions with no coverage around the breakpoints (remaining=1332)
[2026-06-08T08:27:15] Indexing gene sequences 
[2026-06-08T08:27:19] Filtering genes with >=30% identity (remaining=358)
[2026-06-08T08:27:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=180)
[2026-06-08T08:27:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=161)
[2026-06-08T08:27:25] Searching for additional isoforms (remaining=210)
[2026-06-08T08:27:26] Assigning confidence scores to events 
[2026-06-08T08:27:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:27:29] Writing fusions to file 'aih-tih-sc-b567d0-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:27:31] Writing discarded fusions to file 'aih-tih-sc-b567d0-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:27:56] Freeing resources
[2026-06-08T08:28:09] Done (elapsed time=00:08:52, CPU time=00:08:51, peak memory=12.2gb)