[2026-06-08T08:48:26] Launching Arriba 2.4.0
[2026-06-08T08:48:26] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:40] Reading chimeric alignments from '659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9578081)
[2026-06-08T08:55:16] Marking multi-mapping alignments (marked=6034376)
[2026-06-08T08:55:20] Detecting strandedness (reverse)
[2026-06-08T08:55:20] Assigning strands to alignments 
[2026-06-08T08:55:22] Annotating alignments 
[2026-06-08T08:55:56] Filtering duplicates (remaining=3621018)
[2026-06-08T08:56:02] 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=3431637)
[2026-06-08T08:56:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3431637)
[2026-06-08T08:56:06] Filtering viral contigs with expression lower than the top 5 (remaining=3431637)
[2026-06-08T08:56:11] Filtering viral contigs with less than 5% coverage (remaining=3431637)
[2026-06-08T08:56:13] Estimating fragment length (mate gap mean=-88.2507, mate gap stddev=28.6301, read length mean=133.181)
[2026-06-08T08:56:13] Filtering read-through fragments with a distance <=10000bp (remaining=3267996)
[2026-06-08T08:56:15] Filtering inconsistently clipped mates (remaining=3210769)
[2026-06-08T08:56:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3070286)
[2026-06-08T08:56:21] Filtering fragments with small insert size (remaining=3069840)
[2026-06-08T08:56:24] Filtering alignments with long gaps (remaining=3069840)
[2026-06-08T08:56:26] Filtering fragments with both mates in the same gene (remaining=3069246)
[2026-06-08T08:56:28] Filtering fusions arising from hairpin structures (remaining=2904382)
[2026-06-08T08:56:30] Filtering reads with a mismatch p-value <=0.01 (remaining=1202363)
[2026-06-08T08:56:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=452446)
[2026-06-08T08:56:46] Finding fusions and counting supporting reads (total=379516)
[2026-06-08T08:57:01] Merging adjacent fusion breakpoints (remaining=376213)
[2026-06-08T08:57:02] Filtering multi-mapping fusions by alignment score and read support (remaining=231175)
[2026-06-08T08:57:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=229578)
[2026-06-08T08:57:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=123447)
[2026-06-08T08:57:40] Filtering fusions with <2 supporting reads (remaining=15741)
[2026-06-08T08:57:40] Filtering fusions with an e-value >=0.3 (remaining=4602)
[2026-06-08T08:57:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4624)
[2026-06-08T08:57:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4552)
[2026-06-08T08:57:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4553)
[2026-06-08T08:57:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3644)
[2026-06-08T08:57:49] Searching for fusions with spliced split reads (remaining=3711)
[2026-06-08T08:57:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=2657)
[2026-06-08T08:57:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2635)
[2026-06-08T08:57:54] Searching for fusions with >=4 spliced events (remaining=2952)
[2026-06-08T08:57:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=980)
[2026-06-08T08:58:07] Filtering fusions with anchors <=23nt (remaining=791)
[2026-06-08T08:58:08] Filtering end-to-end fusions with low support (remaining=764)
[2026-06-08T08:58:08] Filtering fusions with no coverage around the breakpoints (remaining=734)
[2026-06-08T08:58:08] Indexing gene sequences 
[2026-06-08T08:58:13] Filtering genes with >=30% identity (remaining=293)
[2026-06-08T08:58:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=162)
[2026-06-08T08:58:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=134)
[2026-06-08T08:58:20] Searching for additional isoforms (remaining=159)
[2026-06-08T08:58:21] Assigning confidence scores to events 
[2026-06-08T08:58:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:23] Writing fusions to file '659_cIX-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:25] Writing discarded fusions to file '659_cIX-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:46] Freeing resources
[2026-06-08T08:59:01] Done (elapsed time=00:10:35, CPU time=00:10:33, peak memory=14gb)