[2026-06-08T09:05:28] Launching Arriba 2.4.0
[2026-06-08T09:05:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:05:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:05:40] Reading chimeric alignments from 'aih-tih-sc-776623-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=13926653)
[2026-06-08T09:13:13] Marking multi-mapping alignments (marked=9897002)
[2026-06-08T09:13:19] Detecting strandedness (reverse)
[2026-06-08T09:13:19] Assigning strands to alignments 
[2026-06-08T09:13:22] Annotating alignments 
[2026-06-08T09:14:13] Filtering duplicates (remaining=7472398)
[2026-06-08T09:14:25] 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=6786038)
[2026-06-08T09:14:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6786038)
[2026-06-08T09:14:31] Filtering viral contigs with expression lower than the top 5 (remaining=6786038)
[2026-06-08T09:14:38] Filtering viral contigs with less than 5% coverage (remaining=6786038)
[2026-06-08T09:14:42] Estimating fragment length (mate gap mean=-86.9802, mate gap stddev=29.7998, read length mean=126.859)
[2026-06-08T09:14:42] Filtering read-through fragments with a distance <=10000bp (remaining=6548482)
[2026-06-08T09:14:45] Filtering inconsistently clipped mates (remaining=6453094)
[2026-06-08T09:14:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6300402)
[2026-06-08T09:14:54] Filtering fragments with small insert size (remaining=6299324)
[2026-06-08T09:14:57] Filtering alignments with long gaps (remaining=6299324)
[2026-06-08T09:15:00] Filtering fragments with both mates in the same gene (remaining=6297958)
[2026-06-08T09:15:03] Filtering fusions arising from hairpin structures (remaining=5924915)
[2026-06-08T09:15:06] Filtering reads with a mismatch p-value <=0.01 (remaining=1989983)
[2026-06-08T09:15:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=934424)
[2026-06-08T09:15:35] Finding fusions and counting supporting reads (total=721403)
[2026-06-08T09:15:59] Merging adjacent fusion breakpoints (remaining=712533)
[2026-06-08T09:16:01] Filtering multi-mapping fusions by alignment score and read support (remaining=439912)
[2026-06-08T09:16:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:17:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=437266)
[2026-06-08T09:17:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=287245)
[2026-06-08T09:17:03] Filtering fusions with <2 supporting reads (remaining=31546)
[2026-06-08T09:17:04] Filtering fusions with an e-value >=0.3 (remaining=8247)
[2026-06-08T09:17:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8291)
[2026-06-08T09:17:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8140)
[2026-06-08T09:17:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8140)
[2026-06-08T09:17:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6102)
[2026-06-08T09:17:20] Searching for fusions with spliced split reads (remaining=6230)
[2026-06-08T09:17:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=4081)
[2026-06-08T09:17:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4032)
[2026-06-08T09:17:30] Searching for fusions with >=4 spliced events (remaining=4660)
[2026-06-08T09:17:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1820)
[2026-06-08T09:17:46] Filtering fusions with anchors <=23nt (remaining=1252)
[2026-06-08T09:17:47] Filtering end-to-end fusions with low support (remaining=1131)
[2026-06-08T09:17:48] Filtering fusions with no coverage around the breakpoints (remaining=1098)
[2026-06-08T09:17:49] Indexing gene sequences 
[2026-06-08T09:17:55] Filtering genes with >=30% identity (remaining=361)
[2026-06-08T09:17:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=232)
[2026-06-08T09:18:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=184)
[2026-06-08T09:18:03] Searching for additional isoforms (remaining=219)
[2026-06-08T09:18:05] Assigning confidence scores to events 
[2026-06-08T09:18:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:18:09] Writing fusions to file 'aih-tih-sc-776623-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:18:11] Writing discarded fusions to file 'aih-tih-sc-776623-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:18:46] Freeing resources
[2026-06-08T09:19:09] Done (elapsed time=00:13:41, CPU time=00:13:40, peak memory=19.2gb)