[2026-06-08T08:16:53] Launching Arriba 2.4.0
[2026-06-08T08:16:53] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:06] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:10] Reading chimeric alignments from 'aih-tih-sc-5e5452-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=6067898)
[2026-06-08T08:20:17] Marking multi-mapping alignments (marked=4044678)
[2026-06-08T08:20:19] Detecting strandedness (reverse)
[2026-06-08T08:20:19] Assigning strands to alignments 
[2026-06-08T08:20:20] Annotating alignments 
[2026-06-08T08:20:38] Filtering duplicates (remaining=2128811)
[2026-06-08T08:20:41] 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=1961312)
[2026-06-08T08:20:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1961312)
[2026-06-08T08:20:43] Filtering viral contigs with expression lower than the top 5 (remaining=1961312)
[2026-06-08T08:20:44] Filtering viral contigs with less than 5% coverage (remaining=1961312)
[2026-06-08T08:20:46] Estimating fragment length (mate gap mean=-80.962, mate gap stddev=26.7451, read length mean=116.557)
[2026-06-08T08:20:46] Filtering read-through fragments with a distance <=10000bp (remaining=1851869)
[2026-06-08T08:20:47] Filtering inconsistently clipped mates (remaining=1809201)
[2026-06-08T08:20:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1744846)
[2026-06-08T08:20:49] Filtering fragments with small insert size (remaining=1744291)
[2026-06-08T08:20:50] Filtering alignments with long gaps (remaining=1744291)
[2026-06-08T08:20:51] Filtering fragments with both mates in the same gene (remaining=1743854)
[2026-06-08T08:20:52] Filtering fusions arising from hairpin structures (remaining=1650786)
[2026-06-08T08:20:53] Filtering reads with a mismatch p-value <=0.01 (remaining=593655)
[2026-06-08T08:20:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=230435)
[2026-06-08T08:21:01] Finding fusions and counting supporting reads (total=215183)
[2026-06-08T08:21:08] Merging adjacent fusion breakpoints (remaining=213667)
[2026-06-08T08:21:08] Filtering multi-mapping fusions by alignment score and read support (remaining=121170)
[2026-06-08T08:21:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:21:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=120532)
[2026-06-08T08:21:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=71012)
[2026-06-08T08:21:26] Filtering fusions with <2 supporting reads (remaining=5692)
[2026-06-08T08:21:27] Filtering fusions with an e-value >=0.3 (remaining=1215)
[2026-06-08T08:21:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1237)
[2026-06-08T08:21:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1208)
[2026-06-08T08:21:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1208)
[2026-06-08T08:21:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1192)
[2026-06-08T08:21:31] Searching for fusions with spliced split reads (remaining=1268)
[2026-06-08T08:21:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=952)
[2026-06-08T08:21:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=944)
[2026-06-08T08:21:34] Searching for fusions with >=4 spliced events (remaining=987)
[2026-06-08T08:21:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=324)
[2026-06-08T08:21:46] Filtering fusions with anchors <=23nt (remaining=288)
[2026-06-08T08:21:46] Filtering end-to-end fusions with low support (remaining=279)
[2026-06-08T08:21:46] Filtering fusions with no coverage around the breakpoints (remaining=276)
[2026-06-08T08:21:46] Indexing gene sequences 
[2026-06-08T08:21:48] Filtering genes with >=30% identity (remaining=87)
[2026-06-08T08:21:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=34)
[2026-06-08T08:21:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=34)
[2026-06-08T08:21:50] Searching for additional isoforms (remaining=40)
[2026-06-08T08:21:50] Assigning confidence scores to events 
[2026-06-08T08:21:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:21:51] Writing fusions to file 'aih-tih-sc-5e5452-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:21:52] Writing discarded fusions to file 'aih-tih-sc-5e5452-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:22:02] Freeing resources
[2026-06-08T08:22:11] Done (elapsed time=00:05:18, CPU time=00:05:17, peak memory=10.3gb)