[2026-06-08T09:00:20] Launching Arriba 2.4.0
[2026-06-08T09:00:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:00:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:00:34] Reading chimeric alignments from 'aih-tih-sc-b675f7-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10617569)
[2026-06-08T09:07:49] Marking multi-mapping alignments (marked=6565214)
[2026-06-08T09:07:54] Detecting strandedness (reverse)
[2026-06-08T09:07:54] Assigning strands to alignments 
[2026-06-08T09:07:56] Annotating alignments 
[2026-06-08T09:08:34] Filtering duplicates (remaining=6419498)
[2026-06-08T09:08:42] 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=6113812)
[2026-06-08T09:08:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6113812)
[2026-06-08T09:08:47] Filtering viral contigs with expression lower than the top 5 (remaining=6113812)
[2026-06-08T09:08:52] Filtering viral contigs with less than 5% coverage (remaining=6113812)
[2026-06-08T09:08:55] Estimating fragment length (mate gap mean=-87.1455, mate gap stddev=30.2374, read length mean=135.557)
[2026-06-08T09:08:55] Filtering read-through fragments with a distance <=10000bp (remaining=5725978)
[2026-06-08T09:08:57] Filtering inconsistently clipped mates (remaining=5643433)
[2026-06-08T09:09:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5512639)
[2026-06-08T09:09:05] Filtering fragments with small insert size (remaining=5511981)
[2026-06-08T09:09:07] Filtering alignments with long gaps (remaining=5511980)
[2026-06-08T09:09:09] Filtering fragments with both mates in the same gene (remaining=5510997)
[2026-06-08T09:09:12] Filtering fusions arising from hairpin structures (remaining=5216964)
[2026-06-08T09:09:14] Filtering reads with a mismatch p-value <=0.01 (remaining=2441320)
[2026-06-08T09:09:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=1046857)
[2026-06-08T09:09:40] Finding fusions and counting supporting reads (total=770876)
[2026-06-08T09:09:59] Merging adjacent fusion breakpoints (remaining=765757)
[2026-06-08T09:10:01] Filtering multi-mapping fusions by alignment score and read support (remaining=500960)
[2026-06-08T09:10:37] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:10:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=497604)
[2026-06-08T09:10:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=275133)
[2026-06-08T09:10:47] Filtering fusions with <2 supporting reads (remaining=42938)
[2026-06-08T09:10:48] Filtering fusions with an e-value >=0.3 (remaining=14465)
[2026-06-08T09:10:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14510)
[2026-06-08T09:10:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14431)
[2026-06-08T09:10:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14431)
[2026-06-08T09:10:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9450)
[2026-06-08T09:11:00] Searching for fusions with spliced split reads (remaining=9475)
[2026-06-08T09:11:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=5461)
[2026-06-08T09:11:06] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5383)
[2026-06-08T09:11:07] Searching for fusions with >=4 spliced events (remaining=6503)
[2026-06-08T09:11:08] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2262)
[2026-06-08T09:11:24] Filtering fusions with anchors <=23nt (remaining=1739)
[2026-06-08T09:11:25] Filtering end-to-end fusions with low support (remaining=1660)
[2026-06-08T09:11:25] Filtering fusions with no coverage around the breakpoints (remaining=1610)
[2026-06-08T09:11:26] Indexing gene sequences 
[2026-06-08T09:11:32] Filtering genes with >=30% identity (remaining=470)
[2026-06-08T09:11:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=211)
[2026-06-08T09:11:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=189)
[2026-06-08T09:11:42] Searching for additional isoforms (remaining=242)
[2026-06-08T09:11:43] Assigning confidence scores to events 
[2026-06-08T09:11:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:11:47] Writing fusions to file 'aih-tih-sc-b675f7-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:11:49] Writing discarded fusions to file 'aih-tih-sc-b675f7-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:12:23] Freeing resources
[2026-06-08T09:12:40] Done (elapsed time=00:12:20, CPU time=00:12:18, peak memory=15.3gb)