[2026-06-08T08:16:17] Launching Arriba 2.4.0
[2026-06-08T08:16:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:16:34] Reading chimeric alignments from 'tih_rna_sample_00576_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=7377727)
[2026-06-08T08:21:11] Marking multi-mapping alignments (marked=4776062)
[2026-06-08T08:21:14] Detecting strandedness (reverse)
[2026-06-08T08:21:14] Assigning strands to alignments 
[2026-06-08T08:21:15] Annotating alignments 
[2026-06-08T08:21:37] Filtering duplicates (remaining=4353768)
[2026-06-08T08:21:42] 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=4178631)
[2026-06-08T08:21:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4178631)
[2026-06-08T08:21:45] Filtering viral contigs with expression lower than the top 5 (remaining=4178631)
[2026-06-08T08:21:48] Filtering viral contigs with less than 5% coverage (remaining=4178631)
[2026-06-08T08:21:49] Estimating fragment length (mate gap mean=-86.5253, mate gap stddev=27.4368, read length mean=129.049)
[2026-06-08T08:21:49] Filtering read-through fragments with a distance <=10000bp (remaining=3966126)
[2026-06-08T08:21:51] Filtering inconsistently clipped mates (remaining=3881844)
[2026-06-08T08:21:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3795060)
[2026-06-08T08:21:55] Filtering fragments with small insert size (remaining=3794459)
[2026-06-08T08:21:57] Filtering alignments with long gaps (remaining=3794459)
[2026-06-08T08:21:58] Filtering fragments with both mates in the same gene (remaining=3793780)
[2026-06-08T08:22:00] Filtering fusions arising from hairpin structures (remaining=3531759)
[2026-06-08T08:22:01] Filtering reads with a mismatch p-value <=0.01 (remaining=1750682)
[2026-06-08T08:22:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=573746)
[2026-06-08T08:22:17] Finding fusions and counting supporting reads (total=456605)
[2026-06-08T08:22:29] Merging adjacent fusion breakpoints (remaining=452308)
[2026-06-08T08:22:30] Filtering multi-mapping fusions by alignment score and read support (remaining=266427)
[2026-06-08T08:22:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:22:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=264984)
[2026-06-08T08:22:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=138969)
[2026-06-08T08:22:58] Filtering fusions with <2 supporting reads (remaining=16396)
[2026-06-08T08:22:59] Filtering fusions with an e-value >=0.3 (remaining=4679)
[2026-06-08T08:22:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4727)
[2026-06-08T08:23:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4664)
[2026-06-08T08:23:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4664)
[2026-06-08T08:23:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4247)
[2026-06-08T08:23:07] Searching for fusions with spliced split reads (remaining=4324)
[2026-06-08T08:23:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=2943)
[2026-06-08T08:23:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2915)
[2026-06-08T08:23:12] Searching for fusions with >=4 spliced events (remaining=3278)
[2026-06-08T08:23:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1353)
[2026-06-08T08:23:27] Filtering fusions with anchors <=23nt (remaining=1126)
[2026-06-08T08:23:28] Filtering end-to-end fusions with low support (remaining=1084)
[2026-06-08T08:23:28] Filtering fusions with no coverage around the breakpoints (remaining=1049)
[2026-06-08T08:23:29] Indexing gene sequences 
[2026-06-08T08:23:34] Filtering genes with >=30% identity (remaining=337)
[2026-06-08T08:23:36] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=135)
[2026-06-08T08:23:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=132)
[2026-06-08T08:23:38] Searching for additional isoforms (remaining=152)
[2026-06-08T08:23:39] Assigning confidence scores to events 
[2026-06-08T08:23:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:23:41] Writing fusions to file 'tih_rna_sample_00576_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:23:42] Writing discarded fusions to file 'tih_rna_sample_00576_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:24:03] Freeing resources
[2026-06-08T08:24:16] Done (elapsed time=00:07:59, CPU time=00:07:58, peak memory=11.7gb)