[2026-06-08T08:52:34] Launching Arriba 2.4.0
[2026-06-08T08:52:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:53] Reading chimeric alignments from 'tih_rna_sample_00721_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10184673)
[2026-06-08T09:01:04] Marking multi-mapping alignments (marked=6006587)
[2026-06-08T09:01:08] Detecting strandedness (reverse)
[2026-06-08T09:01:08] Assigning strands to alignments 
[2026-06-08T09:01:10] Annotating alignments 
[2026-06-08T09:01:43] Filtering duplicates (remaining=7305681)
[2026-06-08T09:01:51] 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=7061126)
[2026-06-08T09:01:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7061126)
[2026-06-08T09:01:55] Filtering viral contigs with expression lower than the top 5 (remaining=7061126)
[2026-06-08T09:01:59] Filtering viral contigs with less than 5% coverage (remaining=7061126)
[2026-06-08T09:02:01] Estimating fragment length (mate gap mean=-86.4175, mate gap stddev=30.5815, read length mean=138.884)
[2026-06-08T09:02:01] Filtering read-through fragments with a distance <=10000bp (remaining=6594289)
[2026-06-08T09:02:03] Filtering inconsistently clipped mates (remaining=6509936)
[2026-06-08T09:02:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6358538)
[2026-06-08T09:02:10] Filtering fragments with small insert size (remaining=6358020)
[2026-06-08T09:02:12] Filtering alignments with long gaps (remaining=6358020)
[2026-06-08T09:02:14] Filtering fragments with both mates in the same gene (remaining=6356845)
[2026-06-08T09:02:16] Filtering fusions arising from hairpin structures (remaining=6026923)
[2026-06-08T09:02:18] Filtering reads with a mismatch p-value <=0.01 (remaining=3247545)
[2026-06-08T09:02:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=1257341)
[2026-06-08T09:02:49] Finding fusions and counting supporting reads (total=916112)
[2026-06-08T09:03:06] Merging adjacent fusion breakpoints (remaining=909694)
[2026-06-08T09:03:08] Filtering multi-mapping fusions by alignment score and read support (remaining=606796)
[2026-06-08T09:03:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=603523)
[2026-06-08T09:03:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=352701)
[2026-06-08T09:03:50] Filtering fusions with <2 supporting reads (remaining=46594)
[2026-06-08T09:03:51] Filtering fusions with an e-value >=0.3 (remaining=15544)
[2026-06-08T09:03:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=15619)
[2026-06-08T09:03:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=15535)
[2026-06-08T09:03:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15535)
[2026-06-08T09:03:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9671)
[2026-06-08T09:04:03] Searching for fusions with spliced split reads (remaining=9695)
[2026-06-08T09:04:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=5173)
[2026-06-08T09:04:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5106)
[2026-06-08T09:04:10] Searching for fusions with >=4 spliced events (remaining=6434)
[2026-06-08T09:04:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2730)
[2026-06-08T09:04:29] Filtering fusions with anchors <=23nt (remaining=2270)
[2026-06-08T09:04:30] Filtering end-to-end fusions with low support (remaining=2194)
[2026-06-08T09:04:30] Filtering fusions with no coverage around the breakpoints (remaining=2135)
[2026-06-08T09:04:31] Indexing gene sequences 
[2026-06-08T09:04:39] Filtering genes with >=30% identity (remaining=701)
[2026-06-08T09:04:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=381)
[2026-06-08T09:04:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=262)
[2026-06-08T09:04:53] Searching for additional isoforms (remaining=367)
[2026-06-08T09:04:54] Assigning confidence scores to events 
[2026-06-08T09:04:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:58] Writing fusions to file 'tih_rna_sample_00721_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:02] Writing discarded fusions to file 'tih_rna_sample_00721_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:36] Freeing resources
[2026-06-08T09:05:54] Done (elapsed time=00:13:20, CPU time=00:13:18, peak memory=14.8gb)