[2026-06-08T08:41:22] Launching Arriba 2.4.0
[2026-06-08T08:41:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:37] Reading chimeric alignments from 'aih-tih-sc-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10680823)
[2026-06-08T08:47:36] Marking multi-mapping alignments (marked=7207209)
[2026-06-08T08:47:40] Detecting strandedness (reverse)
[2026-06-08T08:47:40] Assigning strands to alignments 
[2026-06-08T08:47:42] Annotating alignments 
[2026-06-08T08:48:12] Filtering duplicates (remaining=6508073)
[2026-06-08T08:48:18] 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=6172427)
[2026-06-08T08:48:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6172427)
[2026-06-08T08:48:22] Filtering viral contigs with expression lower than the top 5 (remaining=6172427)
[2026-06-08T08:48:26] Filtering viral contigs with less than 5% coverage (remaining=6172427)
[2026-06-08T08:48:28] Estimating fragment length (mate gap mean=-83.7239, mate gap stddev=27.3932, read length mean=122.365)
[2026-06-08T08:48:28] Filtering read-through fragments with a distance <=10000bp (remaining=5768919)
[2026-06-08T08:48:30] Filtering inconsistently clipped mates (remaining=5642530)
[2026-06-08T08:48:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5474133)
[2026-06-08T08:48:36] Filtering fragments with small insert size (remaining=5472629)
[2026-06-08T08:48:37] Filtering alignments with long gaps (remaining=5472629)
[2026-06-08T08:48:39] Filtering fragments with both mates in the same gene (remaining=5471461)
[2026-06-08T08:48:41] Filtering fusions arising from hairpin structures (remaining=5143127)
[2026-06-08T08:48:43] Filtering reads with a mismatch p-value <=0.01 (remaining=2078514)
[2026-06-08T08:48:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=1066965)
[2026-06-08T08:49:05] Finding fusions and counting supporting reads (total=836538)
[2026-06-08T08:49:21] Merging adjacent fusion breakpoints (remaining=828574)
[2026-06-08T08:49:23] Filtering multi-mapping fusions by alignment score and read support (remaining=487591)
[2026-06-08T08:49:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=486328)
[2026-06-08T08:49:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=288153)
[2026-06-08T08:50:00] Filtering fusions with <2 supporting reads (remaining=30517)
[2026-06-08T08:50:01] Filtering fusions with an e-value >=0.3 (remaining=6829)
[2026-06-08T08:50:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6882)
[2026-06-08T08:50:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6788)
[2026-06-08T08:50:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6790)
[2026-06-08T08:50:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6561)
[2026-06-08T08:50:12] Searching for fusions with spliced split reads (remaining=6690)
[2026-06-08T08:50:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=4385)
[2026-06-08T08:50:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4349)
[2026-06-08T08:50:19] Searching for fusions with >=4 spliced events (remaining=5392)
[2026-06-08T08:50:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2370)
[2026-06-08T08:50:35] Filtering fusions with anchors <=23nt (remaining=2001)
[2026-06-08T08:50:36] Filtering end-to-end fusions with low support (remaining=1970)
[2026-06-08T08:50:36] Filtering fusions with no coverage around the breakpoints (remaining=1943)
[2026-06-08T08:50:37] Indexing gene sequences 
[2026-06-08T08:50:44] Filtering genes with >=30% identity (remaining=642)
[2026-06-08T08:50:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=271)
[2026-06-08T08:50:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=214)
[2026-06-08T08:50:53] Searching for additional isoforms (remaining=282)
[2026-06-08T08:50:54] Assigning confidence scores to events 
[2026-06-08T08:50:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:58] Writing fusions to file 'aih-tih-sc-01c779-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:00] Writing discarded fusions to file 'aih-tih-sc-01c779-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:26] Freeing resources
[2026-06-08T08:51:42] Done (elapsed time=00:10:20, CPU time=00:10:19, peak memory=15.5gb)