[2026-06-08T08:34:18] Launching Arriba 2.4.0
[2026-06-08T08:34:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:34] Reading chimeric alignments from 'tih_rna_sample_00451_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10522517)
[2026-06-08T08:40:50] Marking multi-mapping alignments (marked=6607796)
[2026-06-08T08:40:54] Detecting strandedness (reverse)
[2026-06-08T08:40:54] Assigning strands to alignments 
[2026-06-08T08:40:55] Annotating alignments 
[2026-06-08T08:41:26] Filtering duplicates (remaining=4823514)
[2026-06-08T08:41:32] 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=4649928)
[2026-06-08T08:41:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4649928)
[2026-06-08T08:41:36] Filtering viral contigs with expression lower than the top 5 (remaining=4649928)
[2026-06-08T08:41:40] Filtering viral contigs with less than 5% coverage (remaining=4649928)
[2026-06-08T08:41:42] Estimating fragment length (mate gap mean=-88.6269, mate gap stddev=27.4323, read length mean=130.445)
[2026-06-08T08:41:42] Filtering read-through fragments with a distance <=10000bp (remaining=4272316)
[2026-06-08T08:41:44] Filtering inconsistently clipped mates (remaining=4198556)
[2026-06-08T08:41:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4071945)
[2026-06-08T08:41:50] Filtering fragments with small insert size (remaining=4071260)
[2026-06-08T08:41:52] Filtering alignments with long gaps (remaining=4071260)
[2026-06-08T08:41:54] Filtering fragments with both mates in the same gene (remaining=4070445)
[2026-06-08T08:41:57] Filtering fusions arising from hairpin structures (remaining=3868313)
[2026-06-08T08:41:59] Filtering reads with a mismatch p-value <=0.01 (remaining=1658470)
[2026-06-08T08:42:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=818556)
[2026-06-08T08:42:18] Finding fusions and counting supporting reads (total=678751)
[2026-06-08T08:42:33] Merging adjacent fusion breakpoints (remaining=672824)
[2026-06-08T08:42:34] Filtering multi-mapping fusions by alignment score and read support (remaining=402733)
[2026-06-08T08:43:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=400457)
[2026-06-08T08:43:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=214053)
[2026-06-08T08:43:10] Filtering fusions with <2 supporting reads (remaining=26155)
[2026-06-08T08:43:10] Filtering fusions with an e-value >=0.3 (remaining=6425)
[2026-06-08T08:43:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6466)
[2026-06-08T08:43:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6348)
[2026-06-08T08:43:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6348)
[2026-06-08T08:43:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6049)
[2026-06-08T08:43:20] Searching for fusions with spliced split reads (remaining=6176)
[2026-06-08T08:43:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=4034)
[2026-06-08T08:43:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3974)
[2026-06-08T08:43:26] Searching for fusions with >=4 spliced events (remaining=4744)
[2026-06-08T08:43:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1875)
[2026-06-08T08:43:40] Filtering fusions with anchors <=23nt (remaining=1631)
[2026-06-08T08:43:40] Filtering end-to-end fusions with low support (remaining=1591)
[2026-06-08T08:43:41] Filtering fusions with no coverage around the breakpoints (remaining=1546)
[2026-06-08T08:43:41] Indexing gene sequences 
[2026-06-08T08:43:47] Filtering genes with >=30% identity (remaining=471)
[2026-06-08T08:43:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=229)
[2026-06-08T08:43:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=205)
[2026-06-08T08:43:52] Searching for additional isoforms (remaining=259)
[2026-06-08T08:43:53] Assigning confidence scores to events 
[2026-06-08T08:43:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:56] Writing fusions to file 'tih_rna_sample_00451_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:58] Writing discarded fusions to file 'tih_rna_sample_00451_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:21] Freeing resources
[2026-06-08T08:44:37] Done (elapsed time=00:10:19, CPU time=00:10:19, peak memory=15.2gb)