[2026-06-08T08:46:00] Launching Arriba 2.4.0
[2026-06-08T08:46:00] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:10] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:15] Reading chimeric alignments from 'tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=13850545)
[2026-06-08T08:53:17] Marking multi-mapping alignments (marked=9815476)
[2026-06-08T08:53:23] Detecting strandedness (reverse)
[2026-06-08T08:53:23] Assigning strands to alignments 
[2026-06-08T08:53:26] Annotating alignments 
[2026-06-08T08:54:16] Filtering duplicates (remaining=4101339)
[2026-06-08T08:54:24] 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=3648538)
[2026-06-08T08:54:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3648538)
[2026-06-08T08:54:30] Filtering viral contigs with expression lower than the top 5 (remaining=3648538)
[2026-06-08T08:54:36] Filtering viral contigs with less than 5% coverage (remaining=3648538)
[2026-06-08T08:54:40] Estimating fragment length (mate gap mean=-86.1341, mate gap stddev=27.3956, read length mean=123.31)
[2026-06-08T08:54:40] Filtering read-through fragments with a distance <=10000bp (remaining=3447423)
[2026-06-08T08:54:43] Filtering inconsistently clipped mates (remaining=3376662)
[2026-06-08T08:54:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3227641)
[2026-06-08T08:54:52] Filtering fragments with small insert size (remaining=3226483)
[2026-06-08T08:54:55] Filtering alignments with long gaps (remaining=3226482)
[2026-06-08T08:54:58] Filtering fragments with both mates in the same gene (remaining=3225814)
[2026-06-08T08:55:01] Filtering fusions arising from hairpin structures (remaining=3070033)
[2026-06-08T08:55:05] Filtering reads with a mismatch p-value <=0.01 (remaining=1120878)
[2026-06-08T08:55:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=474096)
[2026-06-08T08:55:24] Finding fusions and counting supporting reads (total=408600)
[2026-06-08T08:55:43] Merging adjacent fusion breakpoints (remaining=405045)
[2026-06-08T08:55:44] Filtering multi-mapping fusions by alignment score and read support (remaining=210570)
[2026-06-08T08:56:33] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=209259)
[2026-06-08T08:56:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=122375)
[2026-06-08T08:56:41] Filtering fusions with <2 supporting reads (remaining=11343)
[2026-06-08T08:56:41] Filtering fusions with an e-value >=0.3 (remaining=2749)
[2026-06-08T08:56:42] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2779)
[2026-06-08T08:56:46] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2711)
[2026-06-08T08:56:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2711)
[2026-06-08T08:56:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2559)
[2026-06-08T08:56:53] Searching for fusions with spliced split reads (remaining=2588)
[2026-06-08T08:56:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=1882)
[2026-06-08T08:56:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1865)
[2026-06-08T08:57:00] Searching for fusions with >=4 spliced events (remaining=2090)
[2026-06-08T08:57:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=815)
[2026-06-08T08:57:14] Filtering fusions with anchors <=23nt (remaining=681)
[2026-06-08T08:57:15] Filtering end-to-end fusions with low support (remaining=654)
[2026-06-08T08:57:15] Filtering fusions with no coverage around the breakpoints (remaining=629)
[2026-06-08T08:57:16] Indexing gene sequences 
[2026-06-08T08:57:19] Filtering genes with >=30% identity (remaining=220)
[2026-06-08T08:57:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=107)
[2026-06-08T08:57:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=101)
[2026-06-08T08:57:23] Searching for additional isoforms (remaining=111)
[2026-06-08T08:57:24] Assigning confidence scores to events 
[2026-06-08T08:57:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:26] Writing fusions to file 'tih_rna_sample_00467_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:27] Writing discarded fusions to file 'tih_rna_sample_00467_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:49] Freeing resources
[2026-06-08T08:58:10] Done (elapsed time=00:12:10, CPU time=00:12:09, peak memory=18.4gb)