[2026-06-08T08:13:30] Launching Arriba 2.4.0
[2026-06-08T08:13:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:13:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:13:49] Reading chimeric alignments from 'tih_rna_sample_00410_23H5VFLT4_s34.Aligned.sortedByCoord.out.bam' (total=11848829)
[2026-06-08T08:21:15] Marking multi-mapping alignments (marked=8158801)
[2026-06-08T08:21:20] Detecting strandedness (reverse)
[2026-06-08T08:21:20] Assigning strands to alignments 
[2026-06-08T08:21:23] Annotating alignments 
[2026-06-08T08:22:08] Filtering duplicates (remaining=5349545)
[2026-06-08T08:22:15] 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=4951452)
[2026-06-08T08:22:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4951452)
[2026-06-08T08:22:20] Filtering viral contigs with expression lower than the top 5 (remaining=4951452)
[2026-06-08T08:22:25] Filtering viral contigs with less than 5% coverage (remaining=4951452)
[2026-06-08T08:22:28] Estimating fragment length (mate gap mean=-84.7426, mate gap stddev=29.9834, read length mean=121.949)
[2026-06-08T08:22:28] Filtering read-through fragments with a distance <=10000bp (remaining=4657495)
[2026-06-08T08:22:31] Filtering inconsistently clipped mates (remaining=4560784)
[2026-06-08T08:22:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4016836)
[2026-06-08T08:22:39] Filtering fragments with small insert size (remaining=4015620)
[2026-06-08T08:22:41] Filtering alignments with long gaps (remaining=4015619)
[2026-06-08T08:22:44] Filtering fragments with both mates in the same gene (remaining=4013923)
[2026-06-08T08:22:47] Filtering fusions arising from hairpin structures (remaining=3751520)
[2026-06-08T08:22:49] Filtering reads with a mismatch p-value <=0.01 (remaining=1350862)
[2026-06-08T08:22:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=815717)
[2026-06-08T08:23:10] Finding fusions and counting supporting reads (total=736682)
[2026-06-08T08:23:29] Merging adjacent fusion breakpoints (remaining=732060)
[2026-06-08T08:23:30] Filtering multi-mapping fusions by alignment score and read support (remaining=353277)
[2026-06-08T08:24:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:24:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=350866)
[2026-06-08T08:24:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=237791)
[2026-06-08T08:24:17] Filtering fusions with <2 supporting reads (remaining=19544)
[2026-06-08T08:24:17] Filtering fusions with an e-value >=0.3 (remaining=4438)
[2026-06-08T08:24:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4467)
[2026-06-08T08:24:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4177)
[2026-06-08T08:24:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4177)
[2026-06-08T08:24:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4000)
[2026-06-08T08:24:29] Searching for fusions with spliced split reads (remaining=4087)
[2026-06-08T08:24:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=3026)
[2026-06-08T08:24:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2954)
[2026-06-08T08:24:37] Searching for fusions with >=4 spliced events (remaining=3408)
[2026-06-08T08:24:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1257)
[2026-06-08T08:24:57] Filtering fusions with anchors <=23nt (remaining=954)
[2026-06-08T08:24:57] Filtering end-to-end fusions with low support (remaining=923)
[2026-06-08T08:24:58] Filtering fusions with no coverage around the breakpoints (remaining=909)
[2026-06-08T08:24:59] Indexing gene sequences 
[2026-06-08T08:25:04] Filtering genes with >=30% identity (remaining=270)
[2026-06-08T08:25:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=126)
[2026-06-08T08:25:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=116)
[2026-06-08T08:25:08] Searching for additional isoforms (remaining=151)
[2026-06-08T08:25:10] Assigning confidence scores to events 
[2026-06-08T08:25:13] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:25:14] Writing fusions to file 'tih_rna_sample_00410_23H5VFLT4_s34.arriba.fusions.tsv' 
[2026-06-08T08:25:15] Writing discarded fusions to file 'tih_rna_sample_00410_23H5VFLT4_s34.arriba.fusions.discarded.tsv'
[2026-06-08T08:25:48] Freeing resources
[2026-06-08T08:26:08] Done (elapsed time=00:12:38, CPU time=00:12:37, peak memory=17.1gb)