[2026-06-08T08:06:55] Launching Arriba 2.4.0
[2026-06-08T08:06:55] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:07:10] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:07:16] Reading chimeric alignments from 'tih_rna_sample_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam' (total=12463254)
[2026-06-08T08:15:04] Marking multi-mapping alignments (marked=8915022)
[2026-06-08T08:15:10] Detecting strandedness (reverse)
[2026-06-08T08:15:10] Assigning strands to alignments 
[2026-06-08T08:15:12] Annotating alignments 
[2026-06-08T08:15:58] Filtering duplicates (remaining=5452818)
[2026-06-08T08:16:06] 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=4904852)
[2026-06-08T08:16:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4904852)
[2026-06-08T08:16:11] Filtering viral contigs with expression lower than the top 5 (remaining=4904852)
[2026-06-08T08:16:17] Filtering viral contigs with less than 5% coverage (remaining=4904852)
[2026-06-08T08:16:20] Estimating fragment length (mate gap mean=-79.3915, mate gap stddev=28.8526, read length mean=112.122)
[2026-06-08T08:16:20] Filtering read-through fragments with a distance <=10000bp (remaining=4613900)
[2026-06-08T08:16:22] Filtering inconsistently clipped mates (remaining=4490336)
[2026-06-08T08:16:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3961289)
[2026-06-08T08:16:30] Filtering fragments with small insert size (remaining=3959112)
[2026-06-08T08:16:33] Filtering alignments with long gaps (remaining=3959111)
[2026-06-08T08:16:35] Filtering fragments with both mates in the same gene (remaining=3957560)
[2026-06-08T08:16:38] Filtering fusions arising from hairpin structures (remaining=3663714)
[2026-06-08T08:16:41] Filtering reads with a mismatch p-value <=0.01 (remaining=1120220)
[2026-06-08T08:16:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=740654)
[2026-06-08T08:17:00] Finding fusions and counting supporting reads (total=705608)
[2026-06-08T08:17:18] Merging adjacent fusion breakpoints (remaining=700700)
[2026-06-08T08:17:20] Filtering multi-mapping fusions by alignment score and read support (remaining=317956)
[2026-06-08T08:17:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:18:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=315833)
[2026-06-08T08:18:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=225562)
[2026-06-08T08:18:06] Filtering fusions with <2 supporting reads (remaining=12133)
[2026-06-08T08:18:06] Filtering fusions with an e-value >=0.3 (remaining=2356)
[2026-06-08T08:18:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2404)
[2026-06-08T08:18:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2210)
[2026-06-08T08:18:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2210)
[2026-06-08T08:18:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2184)
[2026-06-08T08:18:19] Searching for fusions with spliced split reads (remaining=2249)
[2026-06-08T08:18:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=1649)
[2026-06-08T08:18:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1615)
[2026-06-08T08:18:26] Searching for fusions with >=4 spliced events (remaining=1841)
[2026-06-08T08:18:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=757)
[2026-06-08T08:18:41] Filtering fusions with anchors <=23nt (remaining=658)
[2026-06-08T08:18:42] Filtering end-to-end fusions with low support (remaining=640)
[2026-06-08T08:18:43] Filtering fusions with no coverage around the breakpoints (remaining=630)
[2026-06-08T08:18:43] Indexing gene sequences 
[2026-06-08T08:18:47] Filtering genes with >=30% identity (remaining=206)
[2026-06-08T08:18:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=106)
[2026-06-08T08:18:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=105)
[2026-06-08T08:18:51] Searching for additional isoforms (remaining=122)
[2026-06-08T08:18:53] Assigning confidence scores to events 
[2026-06-08T08:18:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:18:56] Writing fusions to file 'tih_rna_sample_00115_23H5VFLT4_s35.arriba.fusions.tsv' 
[2026-06-08T08:18:57] Writing discarded fusions to file 'tih_rna_sample_00115_23H5VFLT4_s35.arriba.fusions.discarded.tsv'
[2026-06-08T08:19:29] Freeing resources
[2026-06-08T08:19:50] Done (elapsed time=00:12:55, CPU time=00:12:54, peak memory=17.6gb)