[2026-05-28T00:03:48] Launching Arriba 2.4.0
[2026-05-28T00:03:48] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:56] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:00] Reading chimeric alignments from 'tih_rna_sample_00121_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3404746)
[2026-05-28T00:06:21] Marking multi-mapping alignments (marked=2152058)
[2026-05-28T00:06:23] Detecting strandedness (reverse)
[2026-05-28T00:06:23] Assigning strands to alignments 
[2026-05-28T00:06:23] Annotating alignments 
[2026-05-28T00:06:37] Filtering duplicates (remaining=2368822)
[2026-05-28T00:06:40] 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=2243263)
[2026-05-28T00:06:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2243263)
[2026-05-28T00:06:42] Filtering viral contigs with expression lower than the top 5 (remaining=2243263)
[2026-05-28T00:06:43] Filtering viral contigs with less than 5% coverage (remaining=2243263)
[2026-05-28T00:06:44] Estimating fragment length (mate gap mean=-88.1691, mate gap stddev=28.8829, read length mean=132.935)
[2026-05-28T00:06:45] Filtering read-through fragments with a distance <=10000bp (remaining=2070273)
[2026-05-28T00:06:45] Filtering inconsistently clipped mates (remaining=2026474)
[2026-05-28T00:06:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1973268)
[2026-05-28T00:06:48] Filtering fragments with small insert size (remaining=1972913)
[2026-05-28T00:06:48] Filtering alignments with long gaps (remaining=1972913)
[2026-05-28T00:06:49] Filtering fragments with both mates in the same gene (remaining=1972473)
[2026-05-28T00:06:50] Filtering fusions arising from hairpin structures (remaining=1831742)
[2026-05-28T00:06:51] Filtering reads with a mismatch p-value <=0.01 (remaining=846829)
[2026-05-28T00:06:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=422780)
[2026-05-28T00:07:00] Finding fusions and counting supporting reads (total=337583)
[2026-05-28T00:07:07] Merging adjacent fusion breakpoints (remaining=335462)
[2026-05-28T00:07:07] Filtering multi-mapping fusions by alignment score and read support (remaining=218032)
[2026-05-28T00:07:19] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=216706)
[2026-05-28T00:07:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=115907)
[2026-05-28T00:07:23] Filtering fusions with <2 supporting reads (remaining=17278)
[2026-05-28T00:07:23] Filtering fusions with an e-value >=0.3 (remaining=5634)
[2026-05-28T00:07:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5688)
[2026-05-28T00:07:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5663)
[2026-05-28T00:07:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5663)
[2026-05-28T00:07:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3984)
[2026-05-28T00:07:28] Searching for fusions with spliced split reads (remaining=4025)
[2026-05-28T00:07:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=2734)
[2026-05-28T00:07:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2700)
[2026-05-28T00:07:32] Searching for fusions with >=4 spliced events (remaining=2952)
[2026-05-28T00:07:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=811)
[2026-05-28T00:07:47] Filtering fusions with anchors <=23nt (remaining=657)
[2026-05-28T00:07:47] Filtering end-to-end fusions with low support (remaining=643)
[2026-05-28T00:07:47] Filtering fusions with no coverage around the breakpoints (remaining=630)
[2026-05-28T00:07:48] Indexing gene sequences 
[2026-05-28T00:07:52] Filtering genes with >=30% identity (remaining=230)
[2026-05-28T00:07:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=156)
[2026-05-28T00:07:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=151)
[2026-05-28T00:07:55] Searching for additional isoforms (remaining=180)
[2026-05-28T00:07:56] Assigning confidence scores to events 
[2026-05-28T00:07:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:57] Writing fusions to file 'tih_rna_sample_00121_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:07:58] Writing discarded fusions to file 'tih_rna_sample_00121_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:12] Freeing resources
[2026-05-28T00:08:18] Done (elapsed time=00:04:30, CPU time=00:04:30, peak memory=7.81gb)