[2026-06-08T08:18:45] Launching Arriba 2.4.0
[2026-06-08T08:18:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:18:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:18:59] Reading chimeric alignments from 'aih-tih-sc-a03f86-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=5580157)
[2026-06-08T08:22:45] Marking multi-mapping alignments (marked=3488316)
[2026-06-08T08:22:47] Detecting strandedness (reverse)
[2026-06-08T08:22:47] Assigning strands to alignments 
[2026-06-08T08:22:48] Annotating alignments 
[2026-06-08T08:23:06] Filtering duplicates (remaining=3978071)
[2026-06-08T08:23:10] 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=3811317)
[2026-06-08T08:23:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3811317)
[2026-06-08T08:23:12] Filtering viral contigs with expression lower than the top 5 (remaining=3811317)
[2026-06-08T08:23:14] Filtering viral contigs with less than 5% coverage (remaining=3811317)
[2026-06-08T08:23:16] Estimating fragment length (mate gap mean=-85.883, mate gap stddev=30.7294, read length mean=136.265)
[2026-06-08T08:23:16] Filtering read-through fragments with a distance <=10000bp (remaining=3624190)
[2026-06-08T08:23:17] Filtering inconsistently clipped mates (remaining=3579250)
[2026-06-08T08:23:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3496601)
[2026-06-08T08:23:20] Filtering fragments with small insert size (remaining=3496254)
[2026-06-08T08:23:21] Filtering alignments with long gaps (remaining=3496254)
[2026-06-08T08:23:22] Filtering fragments with both mates in the same gene (remaining=3495601)
[2026-06-08T08:23:23] Filtering fusions arising from hairpin structures (remaining=3354451)
[2026-06-08T08:23:25] Filtering reads with a mismatch p-value <=0.01 (remaining=1714838)
[2026-06-08T08:23:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=568872)
[2026-06-08T08:23:39] Finding fusions and counting supporting reads (total=412021)
[2026-06-08T08:23:48] Merging adjacent fusion breakpoints (remaining=409446)
[2026-06-08T08:23:49] Filtering multi-mapping fusions by alignment score and read support (remaining=267171)
[2026-06-08T08:24:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:24:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=265576)
[2026-06-08T08:24:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=160437)
[2026-06-08T08:24:12] Filtering fusions with <2 supporting reads (remaining=24374)
[2026-06-08T08:24:13] Filtering fusions with an e-value >=0.3 (remaining=9623)
[2026-06-08T08:24:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9666)
[2026-06-08T08:24:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9623)
[2026-06-08T08:24:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9623)
[2026-06-08T08:24:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5176)
[2026-06-08T08:24:20] Searching for fusions with spliced split reads (remaining=5265)
[2026-06-08T08:24:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=3309)
[2026-06-08T08:24:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3261)
[2026-06-08T08:24:24] Searching for fusions with >=4 spliced events (remaining=3598)
[2026-06-08T08:24:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1111)
[2026-06-08T08:24:38] Filtering fusions with anchors <=23nt (remaining=893)
[2026-06-08T08:24:38] Filtering end-to-end fusions with low support (remaining=872)
[2026-06-08T08:24:39] Filtering fusions with no coverage around the breakpoints (remaining=838)
[2026-06-08T08:24:39] Indexing gene sequences 
[2026-06-08T08:24:43] Filtering genes with >=30% identity (remaining=306)
[2026-06-08T08:24:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=181)
[2026-06-08T08:24:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-08T08:24:50] Searching for additional isoforms (remaining=211)
[2026-06-08T08:24:51] Assigning confidence scores to events 
[2026-06-08T08:24:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:24:52] Writing fusions to file 'aih-tih-sc-a03f86-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:24:54] Writing discarded fusions to file 'aih-tih-sc-a03f86-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:25:12] Freeing resources
[2026-06-08T08:25:20] Done (elapsed time=00:06:35, CPU time=00:06:34, peak memory=9.84gb)