[2026-05-28T00:14:44] Launching Arriba 2.4.0
[2026-05-28T00:14:44] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:14:54] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:14:58] Reading chimeric alignments from 'tih_rna_sample_00473_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3303808)
[2026-05-28T00:17:18] Marking multi-mapping alignments (marked=2056617)
[2026-05-28T00:17:19] Detecting strandedness (reverse)
[2026-05-28T00:17:19] Assigning strands to alignments 
[2026-05-28T00:17:20] Annotating alignments 
[2026-05-28T00:17:31] Filtering duplicates (remaining=2372530)
[2026-05-28T00:17:33] 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=2284600)
[2026-05-28T00:17:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2284600)
[2026-05-28T00:17:34] Filtering viral contigs with expression lower than the top 5 (remaining=2284600)
[2026-05-28T00:17:36] Filtering viral contigs with less than 5% coverage (remaining=2284600)
[2026-05-28T00:17:37] Estimating fragment length (mate gap mean=-88.5703, mate gap stddev=29.2102, read length mean=135.673)
[2026-05-28T00:17:37] Filtering read-through fragments with a distance <=10000bp (remaining=2130639)
[2026-05-28T00:17:37] Filtering inconsistently clipped mates (remaining=2094957)
[2026-05-28T00:17:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2055383)
[2026-05-28T00:17:39] Filtering fragments with small insert size (remaining=2055143)
[2026-05-28T00:17:40] Filtering alignments with long gaps (remaining=2055143)
[2026-05-28T00:17:41] Filtering fragments with both mates in the same gene (remaining=2054807)
[2026-05-28T00:17:41] Filtering fusions arising from hairpin structures (remaining=1935334)
[2026-05-28T00:17:42] Filtering reads with a mismatch p-value <=0.01 (remaining=869403)
[2026-05-28T00:17:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=401416)
[2026-05-28T00:17:51] Finding fusions and counting supporting reads (total=305881)
[2026-05-28T00:17:56] Merging adjacent fusion breakpoints (remaining=303351)
[2026-05-28T00:17:57] Filtering multi-mapping fusions by alignment score and read support (remaining=205039)
[2026-05-28T00:18:08] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:18:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=204215)
[2026-05-28T00:18:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=105097)
[2026-05-28T00:18:11] Filtering fusions with <2 supporting reads (remaining=17104)
[2026-05-28T00:18:11] Filtering fusions with an e-value >=0.3 (remaining=5600)
[2026-05-28T00:18:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5639)
[2026-05-28T00:18:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5614)
[2026-05-28T00:18:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5614)
[2026-05-28T00:18:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3443)
[2026-05-28T00:18:15] Searching for fusions with spliced split reads (remaining=3514)
[2026-05-28T00:18:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=2364)
[2026-05-28T00:18:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2333)
[2026-05-28T00:18:18] Searching for fusions with >=4 spliced events (remaining=2594)
[2026-05-28T00:18:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=864)
[2026-05-28T00:18:30] Filtering fusions with anchors <=23nt (remaining=673)
[2026-05-28T00:18:31] Filtering end-to-end fusions with low support (remaining=654)
[2026-05-28T00:18:31] Filtering fusions with no coverage around the breakpoints (remaining=639)
[2026-05-28T00:18:31] Indexing gene sequences 
[2026-05-28T00:18:34] Filtering genes with >=30% identity (remaining=229)
[2026-05-28T00:18:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=135)
[2026-05-28T00:18:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=117)
[2026-05-28T00:18:37] Searching for additional isoforms (remaining=150)
[2026-05-28T00:18:38] Assigning confidence scores to events 
[2026-05-28T00:18:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:18:39] Writing fusions to file 'tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:18:40] Writing discarded fusions to file 'tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:18:52] Freeing resources
[2026-05-28T00:18:58] Done (elapsed time=00:04:14, CPU time=00:04:13, peak memory=7.65gb)