[2026-06-08T08:30:43] Launching Arriba 2.4.0
[2026-06-08T08:30:43] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:59] Reading chimeric alignments from 'tih_rna_sample_00136_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=9117763)
[2026-06-08T08:37:25] Marking multi-mapping alignments (marked=5886076)
[2026-06-08T08:37:28] Detecting strandedness (no)
[2026-06-08T08:37:28] Annotating alignments 
[2026-06-08T08:37:59] Filtering duplicates (remaining=4838441)
[2026-06-08T08:38:03] 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=4597921)
[2026-06-08T08:38:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4597921)
[2026-06-08T08:38:06] Filtering viral contigs with expression lower than the top 5 (remaining=4597921)
[2026-06-08T08:38:10] Filtering viral contigs with less than 5% coverage (remaining=4597921)
[2026-06-08T08:38:11] Estimating fragment length (mate gap mean=-87.1704, mate gap stddev=28.6648, read length mean=132.433)
[2026-06-08T08:38:12] Filtering read-through fragments with a distance <=10000bp (remaining=4316041)
[2026-06-08T08:38:13] Filtering inconsistently clipped mates (remaining=4235938)
[2026-06-08T08:38:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4109735)
[2026-06-08T08:38:17] Filtering fragments with small insert size (remaining=4109105)
[2026-06-08T08:38:19] Filtering alignments with long gaps (remaining=4109105)
[2026-06-08T08:38:20] Filtering fragments with both mates in the same gene (remaining=4108174)
[2026-06-08T08:38:22] Filtering fusions arising from hairpin structures (remaining=3860553)
[2026-06-08T08:38:24] Filtering reads with a mismatch p-value <=0.01 (remaining=1705255)
[2026-06-08T08:38:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=771054)
[2026-06-08T08:38:43] Finding fusions and counting supporting reads (total=593666)
[2026-06-08T08:38:56] Merging adjacent fusion breakpoints (remaining=587441)
[2026-06-08T08:38:57] Filtering multi-mapping fusions by alignment score and read support (remaining=350801)
[2026-06-08T08:39:25] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=346674)
[2026-06-08T08:39:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=191077)
[2026-06-08T08:39:31] Filtering fusions with <2 supporting reads (remaining=27421)
[2026-06-08T08:39:31] Filtering fusions with an e-value >=0.3 (remaining=8426)
[2026-06-08T08:39:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8469)
[2026-06-08T08:39:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8336)
[2026-06-08T08:39:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8337)
[2026-06-08T08:39:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6765)
[2026-06-08T08:39:40] Searching for fusions with spliced split reads (remaining=6781)
[2026-06-08T08:39:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=4302)
[2026-06-08T08:39:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4252)
[2026-06-08T08:39:45] Searching for fusions with >=4 spliced events (remaining=4904)
[2026-06-08T08:39:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1622)
[2026-06-08T08:40:01] Filtering fusions with anchors <=23nt (remaining=1332)
[2026-06-08T08:40:01] Filtering end-to-end fusions with low support (remaining=1291)
[2026-06-08T08:40:02] Filtering fusions with no coverage around the breakpoints (remaining=1263)
[2026-06-08T08:40:02] Indexing gene sequences 
[2026-06-08T08:40:08] Filtering genes with >=30% identity (remaining=450)
[2026-06-08T08:40:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=265)
[2026-06-08T08:40:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=245)
[2026-06-08T08:40:16] Searching for additional isoforms (remaining=313)
[2026-06-08T08:40:17] Assigning confidence scores to events 
[2026-06-08T08:40:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:20] Writing fusions to file 'tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:40:22] Writing discarded fusions to file 'tih_rna_sample_00136_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:45] Freeing resources
[2026-06-08T08:41:00] Done (elapsed time=00:10:17, CPU time=00:10:16, peak memory=13.8gb)