[2026-05-28T00:07:42] Launching Arriba 2.4.0
[2026-05-28T00:07:42] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:07:50] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:07:54] Reading chimeric alignments from 'tih_rna_sample_00164_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=6261542)
[2026-05-28T00:10:24] Marking multi-mapping alignments (marked=4561371)
[2026-05-28T00:10:27] Detecting strandedness (reverse)
[2026-05-28T00:10:27] Assigning strands to alignments 
[2026-05-28T00:10:28] Annotating alignments 
[2026-05-28T00:10:51] Filtering duplicates (remaining=2574867)
[2026-05-28T00:10:55] 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=2244729)
[2026-05-28T00:10:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2244729)
[2026-05-28T00:10:58] Filtering viral contigs with expression lower than the top 5 (remaining=2244729)
[2026-05-28T00:11:00] Filtering viral contigs with less than 5% coverage (remaining=2244729)
[2026-05-28T00:11:02] Estimating fragment length (mate gap mean=-88.5809, mate gap stddev=28.0315, read length mean=125.119)
[2026-05-28T00:11:02] Filtering read-through fragments with a distance <=10000bp (remaining=2164093)
[2026-05-28T00:11:04] Filtering inconsistently clipped mates (remaining=2129567)
[2026-05-28T00:11:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2085108)
[2026-05-28T00:11:08] Filtering fragments with small insert size (remaining=2084495)
[2026-05-28T00:11:09] Filtering alignments with long gaps (remaining=2084495)
[2026-05-28T00:11:11] Filtering fragments with both mates in the same gene (remaining=2084193)
[2026-05-28T00:11:12] Filtering fusions arising from hairpin structures (remaining=1986283)
[2026-05-28T00:11:14] Filtering reads with a mismatch p-value <=0.01 (remaining=586911)
[2026-05-28T00:11:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=272987)
[2026-05-28T00:11:25] Finding fusions and counting supporting reads (total=232187)
[2026-05-28T00:11:35] Merging adjacent fusion breakpoints (remaining=229736)
[2026-05-28T00:11:36] Filtering multi-mapping fusions by alignment score and read support (remaining=135527)
[2026-05-28T00:12:01] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:12:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=134905)
[2026-05-28T00:12:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=79508)
[2026-05-28T00:12:05] Filtering fusions with <2 supporting reads (remaining=7500)
[2026-05-28T00:12:05] Filtering fusions with an e-value >=0.3 (remaining=1640)
[2026-05-28T00:12:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1657)
[2026-05-28T00:12:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1622)
[2026-05-28T00:12:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1622)
[2026-05-28T00:12:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1488)
[2026-05-28T00:12:12] Searching for fusions with spliced split reads (remaining=1569)
[2026-05-28T00:12:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=1254)
[2026-05-28T00:12:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1248)
[2026-05-28T00:12:16] Searching for fusions with >=4 spliced events (remaining=1348)
[2026-05-28T00:12:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=550)
[2026-05-28T00:12:28] Filtering fusions with anchors <=23nt (remaining=351)
[2026-05-28T00:12:28] Filtering end-to-end fusions with low support (remaining=309)
[2026-05-28T00:12:29] Filtering fusions with no coverage around the breakpoints (remaining=296)
[2026-05-28T00:12:29] Indexing gene sequences 
[2026-05-28T00:12:31] Filtering genes with >=30% identity (remaining=96)
[2026-05-28T00:12:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=57)
[2026-05-28T00:12:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=57)
[2026-05-28T00:12:33] Searching for additional isoforms (remaining=61)
[2026-05-28T00:12:34] Assigning confidence scores to events 
[2026-05-28T00:12:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:12:36] Writing fusions to file 'tih_rna_sample_00164_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:12:36] Writing discarded fusions to file 'tih_rna_sample_00164_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:12:52] Freeing resources
[2026-05-28T00:13:03] Done (elapsed time=00:05:21, CPU time=00:05:20, peak memory=10.8gb)