[2026-05-28T00:04:57] Launching Arriba 2.4.0
[2026-05-28T00:04:57] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:06] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:05:10] Reading chimeric alignments from 'tih_rna_sample_00464_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3392126)
[2026-05-28T00:07:28] Marking multi-mapping alignments (marked=2117581)
[2026-05-28T00:07:30] Detecting strandedness (reverse)
[2026-05-28T00:07:30] Assigning strands to alignments 
[2026-05-28T00:07:31] Annotating alignments 
[2026-05-28T00:07:45] Filtering duplicates (remaining=1932601)
[2026-05-28T00:07:47] 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=1857715)
[2026-05-28T00:07:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1857715)
[2026-05-28T00:07:49] Filtering viral contigs with expression lower than the top 5 (remaining=1857715)
[2026-05-28T00:07:50] Filtering viral contigs with less than 5% coverage (remaining=1857715)
[2026-05-28T00:07:51] Estimating fragment length (mate gap mean=-87.305, mate gap stddev=28.1352, read length mean=129.736)
[2026-05-28T00:07:51] Filtering read-through fragments with a distance <=10000bp (remaining=1720148)
[2026-05-28T00:07:52] Filtering inconsistently clipped mates (remaining=1690537)
[2026-05-28T00:07:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1638703)
[2026-05-28T00:07:54] Filtering fragments with small insert size (remaining=1638347)
[2026-05-28T00:07:55] Filtering alignments with long gaps (remaining=1638347)
[2026-05-28T00:07:55] Filtering fragments with both mates in the same gene (remaining=1638043)
[2026-05-28T00:07:56] Filtering fusions arising from hairpin structures (remaining=1548714)
[2026-05-28T00:07:57] Filtering reads with a mismatch p-value <=0.01 (remaining=676334)
[2026-05-28T00:08:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=334831)
[2026-05-28T00:08:04] Finding fusions and counting supporting reads (total=286985)
[2026-05-28T00:08:11] Merging adjacent fusion breakpoints (remaining=285506)
[2026-05-28T00:08:11] Filtering multi-mapping fusions by alignment score and read support (remaining=172284)
[2026-05-28T00:08:23] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=171363)
[2026-05-28T00:08:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90511)
[2026-05-28T00:08:26] Filtering fusions with <2 supporting reads (remaining=11124)
[2026-05-28T00:08:26] Filtering fusions with an e-value >=0.3 (remaining=3209)
[2026-05-28T00:08:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3244)
[2026-05-28T00:08:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3207)
[2026-05-28T00:08:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3207)
[2026-05-28T00:08:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2815)
[2026-05-28T00:08:30] Searching for fusions with spliced split reads (remaining=2846)
[2026-05-28T00:08:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=2098)
[2026-05-28T00:08:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2067)
[2026-05-28T00:08:33] Searching for fusions with >=4 spliced events (remaining=2222)
[2026-05-28T00:08:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=718)
[2026-05-28T00:08:46] Filtering fusions with anchors <=23nt (remaining=580)
[2026-05-28T00:08:47] Filtering end-to-end fusions with low support (remaining=559)
[2026-05-28T00:08:47] Filtering fusions with no coverage around the breakpoints (remaining=532)
[2026-05-28T00:08:47] Indexing gene sequences 
[2026-05-28T00:08:50] Filtering genes with >=30% identity (remaining=180)
[2026-05-28T00:08:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=104)
[2026-05-28T00:08:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=104)
[2026-05-28T00:08:52] Searching for additional isoforms (remaining=119)
[2026-05-28T00:08:52] Assigning confidence scores to events 
[2026-05-28T00:08:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:54] Writing fusions to file 'tih_rna_sample_00464_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:08:54] Writing discarded fusions to file 'tih_rna_sample_00464_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:07] Freeing resources
[2026-05-28T00:09:15] Done (elapsed time=00:04:18, CPU time=00:04:17, peak memory=7.71gb)