[2026-06-08T08:50:33] Launching Arriba 2.4.0
[2026-06-08T08:50:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:47] Reading chimeric alignments from 'tih_rna_sample_00087_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9774278)
[2026-06-08T08:57:39] Marking multi-mapping alignments (marked=6239401)
[2026-06-08T08:57:43] Detecting strandedness (reverse)
[2026-06-08T08:57:43] Assigning strands to alignments 
[2026-06-08T08:57:45] Annotating alignments 
[2026-06-08T08:58:20] Filtering duplicates (remaining=5710846)
[2026-06-08T08:58:26] 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=5454494)
[2026-06-08T08:58:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5454494)
[2026-06-08T08:58:30] Filtering viral contigs with expression lower than the top 5 (remaining=5454494)
[2026-06-08T08:58:34] Filtering viral contigs with less than 5% coverage (remaining=5454494)
[2026-06-08T08:58:37] Estimating fragment length (mate gap mean=-88.077, mate gap stddev=28.5434, read length mean=134.575)
[2026-06-08T08:58:37] Filtering read-through fragments with a distance <=10000bp (remaining=5075233)
[2026-06-08T08:58:39] Filtering inconsistently clipped mates (remaining=4993273)
[2026-06-08T08:58:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4859021)
[2026-06-08T08:58:45] Filtering fragments with small insert size (remaining=4858401)
[2026-06-08T08:58:46] Filtering alignments with long gaps (remaining=4858401)
[2026-06-08T08:58:48] Filtering fragments with both mates in the same gene (remaining=4857344)
[2026-06-08T08:58:51] Filtering fusions arising from hairpin structures (remaining=4565629)
[2026-06-08T08:58:53] Filtering reads with a mismatch p-value <=0.01 (remaining=2157839)
[2026-06-08T08:59:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=1070671)
[2026-06-08T08:59:15] Finding fusions and counting supporting reads (total=802948)
[2026-06-08T08:59:31] Merging adjacent fusion breakpoints (remaining=792619)
[2026-06-08T08:59:33] Filtering multi-mapping fusions by alignment score and read support (remaining=471650)
[2026-06-08T09:00:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=467414)
[2026-06-08T09:00:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=253351)
[2026-06-08T09:00:13] Filtering fusions with <2 supporting reads (remaining=38947)
[2026-06-08T09:00:13] Filtering fusions with an e-value >=0.3 (remaining=12112)
[2026-06-08T09:00:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12152)
[2026-06-08T09:00:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12008)
[2026-06-08T09:00:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12008)
[2026-06-08T09:00:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9182)
[2026-06-08T09:00:24] Searching for fusions with spliced split reads (remaining=9228)
[2026-06-08T09:00:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=5258)
[2026-06-08T09:00:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5198)
[2026-06-08T09:00:31] Searching for fusions with >=4 spliced events (remaining=6278)
[2026-06-08T09:00:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2338)
[2026-06-08T09:00:46] Filtering fusions with anchors <=23nt (remaining=1978)
[2026-06-08T09:00:47] Filtering end-to-end fusions with low support (remaining=1910)
[2026-06-08T09:00:47] Filtering fusions with no coverage around the breakpoints (remaining=1852)
[2026-06-08T09:00:48] Indexing gene sequences 
[2026-06-08T09:00:54] Filtering genes with >=30% identity (remaining=538)
[2026-06-08T09:00:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=213)
[2026-06-08T09:01:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=200)
[2026-06-08T09:01:05] Searching for additional isoforms (remaining=285)
[2026-06-08T09:01:06] Assigning confidence scores to events 
[2026-06-08T09:01:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:09] Writing fusions to file 'tih_rna_sample_00087_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:12] Writing discarded fusions to file 'tih_rna_sample_00087_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:40] Freeing resources
[2026-06-08T09:01:57] Done (elapsed time=00:11:24, CPU time=00:11:23, peak memory=14.5gb)