[2026-06-08T08:52:22] Launching Arriba 2.4.0
[2026-06-08T08:52:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:42] Reading chimeric alignments from 'tih_rna_sample_00462_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=9292709)
[2026-06-08T09:03:39] Marking multi-mapping alignments (marked=5648743)
[2026-06-08T09:03:44] Detecting strandedness (reverse)
[2026-06-08T09:03:44] Assigning strands to alignments 
[2026-06-08T09:03:46] Annotating alignments 
[2026-06-08T09:04:22] Filtering duplicates (remaining=5683698)
[2026-06-08T09:04:31] 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=5444258)
[2026-06-08T09:04:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5444258)
[2026-06-08T09:04:35] Filtering viral contigs with expression lower than the top 5 (remaining=5444258)
[2026-06-08T09:04:39] Filtering viral contigs with less than 5% coverage (remaining=5444258)
[2026-06-08T09:04:41] Estimating fragment length (mate gap mean=-89.072, mate gap stddev=29.4192, read length mean=136.533)
[2026-06-08T09:04:42] Filtering read-through fragments with a distance <=10000bp (remaining=5042282)
[2026-06-08T09:04:44] Filtering inconsistently clipped mates (remaining=4965652)
[2026-06-08T09:04:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4856163)
[2026-06-08T09:04:50] Filtering fragments with small insert size (remaining=4855521)
[2026-06-08T09:04:52] Filtering alignments with long gaps (remaining=4855521)
[2026-06-08T09:04:54] Filtering fragments with both mates in the same gene (remaining=4854529)
[2026-06-08T09:04:56] Filtering fusions arising from hairpin structures (remaining=4579667)
[2026-06-08T09:04:58] Filtering reads with a mismatch p-value <=0.01 (remaining=2028589)
[2026-06-08T09:05:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=930963)
[2026-06-08T09:05:23] Finding fusions and counting supporting reads (total=721541)
[2026-06-08T09:05:40] Merging adjacent fusion breakpoints (remaining=715122)
[2026-06-08T09:05:41] Filtering multi-mapping fusions by alignment score and read support (remaining=487872)
[2026-06-08T09:06:16] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:06:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=485673)
[2026-06-08T09:06:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=248069)
[2026-06-08T09:06:25] Filtering fusions with <2 supporting reads (remaining=37758)
[2026-06-08T09:06:25] Filtering fusions with an e-value >=0.3 (remaining=12122)
[2026-06-08T09:06:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12164)
[2026-06-08T09:06:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12068)
[2026-06-08T09:06:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12068)
[2026-06-08T09:06:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7902)
[2026-06-08T09:06:36] Searching for fusions with spliced split reads (remaining=8017)
[2026-06-08T09:06:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=4997)
[2026-06-08T09:06:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4916)
[2026-06-08T09:06:43] Searching for fusions with >=4 spliced events (remaining=5880)
[2026-06-08T09:06:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2215)
[2026-06-08T09:07:05] Filtering fusions with anchors <=23nt (remaining=1685)
[2026-06-08T09:07:06] Filtering end-to-end fusions with low support (remaining=1639)
[2026-06-08T09:07:06] Filtering fusions with no coverage around the breakpoints (remaining=1601)
[2026-06-08T09:07:07] Indexing gene sequences 
[2026-06-08T09:07:14] Filtering genes with >=30% identity (remaining=492)
[2026-06-08T09:07:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=220)
[2026-06-08T09:07:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-08T09:07:23] Searching for additional isoforms (remaining=257)
[2026-06-08T09:07:24] Assigning confidence scores to events 
[2026-06-08T09:07:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:07:27] Writing fusions to file 'tih_rna_sample_00462_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:07:29] Writing discarded fusions to file 'tih_rna_sample_00462_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:00] Freeing resources
[2026-06-08T09:08:16] Done (elapsed time=00:15:54, CPU time=00:15:52, peak memory=14gb)