[2026-06-08T08:51:38] Launching Arriba 2.4.0
[2026-06-08T08:51:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:53] Reading chimeric alignments from 'tih_rna_sample_00145_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=11484534)
[2026-06-08T08:58:52] Marking multi-mapping alignments (marked=7209908)
[2026-06-08T08:58:58] Detecting strandedness (reverse)
[2026-06-08T08:58:58] Assigning strands to alignments 
[2026-06-08T08:59:00] Annotating alignments 
[2026-06-08T08:59:43] Filtering duplicates (remaining=3372376)
[2026-06-08T08:59:49] 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=3194304)
[2026-06-08T08:59:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3194304)
[2026-06-08T08:59:55] Filtering viral contigs with expression lower than the top 5 (remaining=3194304)
[2026-06-08T09:00:00] Filtering viral contigs with less than 5% coverage (remaining=3194304)
[2026-06-08T09:00:03] Estimating fragment length (mate gap mean=-89.6657, mate gap stddev=26.8901, read length mean=129.839)
[2026-06-08T09:00:03] Filtering read-through fragments with a distance <=10000bp (remaining=2970484)
[2026-06-08T09:00:06] Filtering inconsistently clipped mates (remaining=2915881)
[2026-06-08T09:00:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2808331)
[2026-06-08T09:00:13] Filtering fragments with small insert size (remaining=2807607)
[2026-06-08T09:00:15] Filtering alignments with long gaps (remaining=2807607)
[2026-06-08T09:00:18] Filtering fragments with both mates in the same gene (remaining=2807037)
[2026-06-08T09:00:21] Filtering fusions arising from hairpin structures (remaining=2683807)
[2026-06-08T09:00:24] Filtering reads with a mismatch p-value <=0.01 (remaining=1042947)
[2026-06-08T09:00:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=464233)
[2026-06-08T09:00:43] Finding fusions and counting supporting reads (total=418154)
[2026-06-08T09:01:06] Merging adjacent fusion breakpoints (remaining=413943)
[2026-06-08T09:01:07] Filtering multi-mapping fusions by alignment score and read support (remaining=239257)
[2026-06-08T09:01:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=237980)
[2026-06-08T09:01:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=126348)
[2026-06-08T09:01:58] Filtering fusions with <2 supporting reads (remaining=12053)
[2026-06-08T09:01:59] Filtering fusions with an e-value >=0.3 (remaining=2814)
[2026-06-08T09:01:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2845)
[2026-06-08T09:02:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2776)
[2026-06-08T09:02:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2776)
[2026-06-08T09:02:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2656)
[2026-06-08T09:02:11] Searching for fusions with spliced split reads (remaining=2685)
[2026-06-08T09:02:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=1991)
[2026-06-08T09:02:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1972)
[2026-06-08T09:02:18] Searching for fusions with >=4 spliced events (remaining=2201)
[2026-06-08T09:02:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=851)
[2026-06-08T09:02:32] Filtering fusions with anchors <=23nt (remaining=713)
[2026-06-08T09:02:33] Filtering end-to-end fusions with low support (remaining=686)
[2026-06-08T09:02:33] Filtering fusions with no coverage around the breakpoints (remaining=663)
[2026-06-08T09:02:34] Indexing gene sequences 
[2026-06-08T09:02:37] Filtering genes with >=30% identity (remaining=238)
[2026-06-08T09:02:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=93)
[2026-06-08T09:02:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=90)
[2026-06-08T09:02:41] Searching for additional isoforms (remaining=105)
[2026-06-08T09:02:42] Assigning confidence scores to events 
[2026-06-08T09:02:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:44] Writing fusions to file 'tih_rna_sample_00145_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:02:45] Writing discarded fusions to file 'tih_rna_sample_00145_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:05] Freeing resources
[2026-06-08T09:03:26] Done (elapsed time=00:11:48, CPU time=00:11:47, peak memory=16gb)