[2026-05-28T00:07:44] Launching Arriba 2.4.0
[2026-05-28T00:07:44] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:07:52] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:07:56] Reading chimeric alignments from 'tih_rna_sample_00479_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3228351)
[2026-05-28T00:10:20] Marking multi-mapping alignments (marked=1971827)
[2026-05-28T00:10:21] Detecting strandedness (reverse)
[2026-05-28T00:10:21] Assigning strands to alignments 
[2026-05-28T00:10:22] Annotating alignments 
[2026-05-28T00:10:35] Filtering duplicates (remaining=2190351)
[2026-05-28T00:10:38] 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=2093032)
[2026-05-28T00:10:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2093032)
[2026-05-28T00:10:39] Filtering viral contigs with expression lower than the top 5 (remaining=2093032)
[2026-05-28T00:10:41] Filtering viral contigs with less than 5% coverage (remaining=2093032)
[2026-05-28T00:10:42] Estimating fragment length (mate gap mean=-88.6784, mate gap stddev=28.0513, read length mean=134.887)
[2026-05-28T00:10:42] Filtering read-through fragments with a distance <=10000bp (remaining=1932961)
[2026-05-28T00:10:43] Filtering inconsistently clipped mates (remaining=1901342)
[2026-05-28T00:10:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1861219)
[2026-05-28T00:10:45] Filtering fragments with small insert size (remaining=1860829)
[2026-05-28T00:10:46] Filtering alignments with long gaps (remaining=1860829)
[2026-05-28T00:10:47] Filtering fragments with both mates in the same gene (remaining=1860483)
[2026-05-28T00:10:48] Filtering fusions arising from hairpin structures (remaining=1760887)
[2026-05-28T00:10:49] Filtering reads with a mismatch p-value <=0.01 (remaining=832672)
[2026-05-28T00:10:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=416421)
[2026-05-28T00:10:59] Finding fusions and counting supporting reads (total=339864)
[2026-05-28T00:11:07] Merging adjacent fusion breakpoints (remaining=337860)
[2026-05-28T00:11:08] Filtering multi-mapping fusions by alignment score and read support (remaining=216299)
[2026-05-28T00:11:20] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:11:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=214800)
[2026-05-28T00:11:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=111927)
[2026-05-28T00:11:24] Filtering fusions with <2 supporting reads (remaining=16737)
[2026-05-28T00:11:25] Filtering fusions with an e-value >=0.3 (remaining=5056)
[2026-05-28T00:11:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5095)
[2026-05-28T00:11:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5062)
[2026-05-28T00:11:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5062)
[2026-05-28T00:11:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4091)
[2026-05-28T00:11:29] Searching for fusions with spliced split reads (remaining=4151)
[2026-05-28T00:11:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=2857)
[2026-05-28T00:11:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2839)
[2026-05-28T00:11:32] Searching for fusions with >=4 spliced events (remaining=3197)
[2026-05-28T00:11:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1033)
[2026-05-28T00:11:45] Filtering fusions with anchors <=23nt (remaining=886)
[2026-05-28T00:11:45] Filtering end-to-end fusions with low support (remaining=869)
[2026-05-28T00:11:45] Filtering fusions with no coverage around the breakpoints (remaining=840)
[2026-05-28T00:11:46] Indexing gene sequences 
[2026-05-28T00:11:53] Filtering genes with >=30% identity (remaining=370)
[2026-05-28T00:11:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=275)
[2026-05-28T00:11:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=228)
[2026-05-28T00:11:59] Searching for additional isoforms (remaining=315)
[2026-05-28T00:11:59] Assigning confidence scores to events 
[2026-05-28T00:12:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:12:01] Writing fusions to file 'tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:12:04] Writing discarded fusions to file 'tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:12:19] Freeing resources
[2026-05-28T00:12:26] Done (elapsed time=00:04:42, CPU time=00:04:41, peak memory=7.57gb)