[2026-06-08T08:47:27] Launching Arriba 2.4.0
[2026-06-08T08:47:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:44] Reading chimeric alignments from 'aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9046260)
[2026-06-08T08:55:07] Marking multi-mapping alignments (marked=5694752)
[2026-06-08T08:55:11] Detecting strandedness (reverse)
[2026-06-08T08:55:11] Assigning strands to alignments 
[2026-06-08T08:55:13] Annotating alignments 
[2026-06-08T08:55:44] Filtering duplicates (remaining=6598299)
[2026-06-08T08:55:52] 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=6246683)
[2026-06-08T08:55:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6246683)
[2026-06-08T08:55:56] Filtering viral contigs with expression lower than the top 5 (remaining=6246683)
[2026-06-08T08:56:00] Filtering viral contigs with less than 5% coverage (remaining=6246683)
[2026-06-08T08:56:02] Estimating fragment length (mate gap mean=-85.7222, mate gap stddev=29.4679, read length mean=131.528)
[2026-06-08T08:56:02] Filtering read-through fragments with a distance <=10000bp (remaining=5830014)
[2026-06-08T08:56:04] Filtering inconsistently clipped mates (remaining=5715547)
[2026-06-08T08:56:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5551426)
[2026-06-08T08:56:10] Filtering fragments with small insert size (remaining=5550665)
[2026-06-08T08:56:12] Filtering alignments with long gaps (remaining=5550665)
[2026-06-08T08:56:14] Filtering fragments with both mates in the same gene (remaining=5549472)
[2026-06-08T08:56:16] Filtering fusions arising from hairpin structures (remaining=5165721)
[2026-06-08T08:56:19] Filtering reads with a mismatch p-value <=0.01 (remaining=2487294)
[2026-06-08T08:56:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=1305927)
[2026-06-08T08:56:44] Finding fusions and counting supporting reads (total=1004172)
[2026-06-08T08:57:00] Merging adjacent fusion breakpoints (remaining=996251)
[2026-06-08T08:57:02] Filtering multi-mapping fusions by alignment score and read support (remaining=630976)
[2026-06-08T08:57:33] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=628207)
[2026-06-08T08:57:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=399116)
[2026-06-08T08:57:42] Filtering fusions with <2 supporting reads (remaining=41088)
[2026-06-08T08:57:43] Filtering fusions with an e-value >=0.3 (remaining=11478)
[2026-06-08T08:57:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11544)
[2026-06-08T08:57:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11423)
[2026-06-08T08:57:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11423)
[2026-06-08T08:57:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8897)
[2026-06-08T08:57:55] Searching for fusions with spliced split reads (remaining=8914)
[2026-06-08T08:57:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=5024)
[2026-06-08T08:58:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4949)
[2026-06-08T08:58:02] Searching for fusions with >=4 spliced events (remaining=6034)
[2026-06-08T08:58:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2436)
[2026-06-08T08:58:18] Filtering fusions with anchors <=23nt (remaining=2025)
[2026-06-08T08:58:18] Filtering end-to-end fusions with low support (remaining=1965)
[2026-06-08T08:58:19] Filtering fusions with no coverage around the breakpoints (remaining=1919)
[2026-06-08T08:58:20] Indexing gene sequences 
[2026-06-08T08:58:26] Filtering genes with >=30% identity (remaining=551)
[2026-06-08T08:58:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=258)
[2026-06-08T08:58:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=220)
[2026-06-08T08:58:45] Searching for additional isoforms (remaining=298)
[2026-06-08T08:58:46] Assigning confidence scores to events 
[2026-06-08T08:58:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:50] Writing fusions to file 'aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:53] Writing discarded fusions to file 'aih-tih-sc-5ceb9a-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:26] Freeing resources
[2026-06-08T08:59:41] Done (elapsed time=00:12:14, CPU time=00:12:13, peak memory=13.9gb)