[2026-05-28T00:03:56] Launching Arriba 2.4.0
[2026-05-28T00:03:56] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:04:05] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:09] Reading chimeric alignments from 'tih_rna_sample_00145_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3768319)
[2026-05-28T00:06:27] Marking multi-mapping alignments (marked=2404304)
[2026-05-28T00:06:28] Detecting strandedness (reverse)
[2026-05-28T00:06:28] Assigning strands to alignments 
[2026-05-28T00:06:29] Annotating alignments 
[2026-05-28T00:06:43] Filtering duplicates (remaining=2293192)
[2026-05-28T00:06:45] 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=2177561)
[2026-05-28T00:06:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2177561)
[2026-05-28T00:06:47] Filtering viral contigs with expression lower than the top 5 (remaining=2177561)
[2026-05-28T00:06:48] Filtering viral contigs with less than 5% coverage (remaining=2177561)
[2026-05-28T00:06:49] Estimating fragment length (mate gap mean=-85.5149, mate gap stddev=26.9314, read length mean=124.492)
[2026-05-28T00:06:49] Filtering read-through fragments with a distance <=10000bp (remaining=1969052)
[2026-05-28T00:06:50] Filtering inconsistently clipped mates (remaining=1927327)
[2026-05-28T00:06:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1883451)
[2026-05-28T00:06:52] Filtering fragments with small insert size (remaining=1882901)
[2026-05-28T00:06:53] Filtering alignments with long gaps (remaining=1882901)
[2026-05-28T00:06:54] Filtering fragments with both mates in the same gene (remaining=1882559)
[2026-05-28T00:06:55] Filtering fusions arising from hairpin structures (remaining=1767582)
[2026-05-28T00:06:56] Filtering reads with a mismatch p-value <=0.01 (remaining=751271)
[2026-05-28T00:07:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=386824)
[2026-05-28T00:07:05] Finding fusions and counting supporting reads (total=343629)
[2026-05-28T00:07:12] Merging adjacent fusion breakpoints (remaining=340154)
[2026-05-28T00:07:13] Filtering multi-mapping fusions by alignment score and read support (remaining=207554)
[2026-05-28T00:07:26] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=206638)
[2026-05-28T00:07:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=103904)
[2026-05-28T00:07:29] Filtering fusions with <2 supporting reads (remaining=10646)
[2026-05-28T00:07:30] Filtering fusions with an e-value >=0.3 (remaining=2705)
[2026-05-28T00:07:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2753)
[2026-05-28T00:07:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2721)
[2026-05-28T00:07:32] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2721)
[2026-05-28T00:07:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2600)
[2026-05-28T00:07:34] Searching for fusions with spliced split reads (remaining=2621)
[2026-05-28T00:07:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=1963)
[2026-05-28T00:07:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1950)
[2026-05-28T00:07:37] Searching for fusions with >=4 spliced events (remaining=2109)
[2026-05-28T00:07:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=767)
[2026-05-28T00:07:50] Filtering fusions with anchors <=23nt (remaining=631)
[2026-05-28T00:07:50] Filtering end-to-end fusions with low support (remaining=612)
[2026-05-28T00:07:50] Filtering fusions with no coverage around the breakpoints (remaining=596)
[2026-05-28T00:07:51] Indexing gene sequences 
[2026-05-28T00:07:54] Filtering genes with >=30% identity (remaining=195)
[2026-05-28T00:07:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=92)
[2026-05-28T00:07:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=92)
[2026-05-28T00:07:56] Searching for additional isoforms (remaining=104)
[2026-05-28T00:07:57] Assigning confidence scores to events 
[2026-05-28T00:07:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:58] Writing fusions to file 'tih_rna_sample_00145_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:07:59] Writing discarded fusions to file 'tih_rna_sample_00145_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:12] Freeing resources
[2026-05-28T00:08:19] Done (elapsed time=00:04:23, CPU time=00:04:22, peak memory=8.13gb)