[2026-06-08T09:06:26] Launching Arriba 2.4.0
[2026-06-08T09:06:26] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:06:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:06:39] Reading chimeric alignments from '659_bUW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9648203)
[2026-06-08T09:13:44] Marking multi-mapping alignments (marked=6238345)
[2026-06-08T09:13:49] Detecting strandedness (reverse)
[2026-06-08T09:13:49] Assigning strands to alignments 
[2026-06-08T09:13:51] Annotating alignments 
[2026-06-08T09:14:25] Filtering duplicates (remaining=5045372)
[2026-06-08T09:14:31] 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=4868779)
[2026-06-08T09:14:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4868779)
[2026-06-08T09:14:35] Filtering viral contigs with expression lower than the top 5 (remaining=4868779)
[2026-06-08T09:14:40] Filtering viral contigs with less than 5% coverage (remaining=4868779)
[2026-06-08T09:14:42] Estimating fragment length (mate gap mean=-87.2429, mate gap stddev=28.8688, read length mean=134.921)
[2026-06-08T09:14:42] Filtering read-through fragments with a distance <=10000bp (remaining=4491572)
[2026-06-08T09:14:44] Filtering inconsistently clipped mates (remaining=4430204)
[2026-06-08T09:14:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4303168)
[2026-06-08T09:14:51] Filtering fragments with small insert size (remaining=4302718)
[2026-06-08T09:14:53] Filtering alignments with long gaps (remaining=4302718)
[2026-06-08T09:14:55] Filtering fragments with both mates in the same gene (remaining=4301941)
[2026-06-08T09:14:57] Filtering fusions arising from hairpin structures (remaining=4058906)
[2026-06-08T09:15:00] Filtering reads with a mismatch p-value <=0.01 (remaining=1825014)
[2026-06-08T09:15:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=801812)
[2026-06-08T09:15:20] Finding fusions and counting supporting reads (total=614138)
[2026-06-08T09:15:37] Merging adjacent fusion breakpoints (remaining=605596)
[2026-06-08T09:15:38] Filtering multi-mapping fusions by alignment score and read support (remaining=389587)
[2026-06-08T09:16:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:16:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=387823)
[2026-06-08T09:16:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=175808)
[2026-06-08T09:16:20] Filtering fusions with <2 supporting reads (remaining=26395)
[2026-06-08T09:16:21] Filtering fusions with an e-value >=0.3 (remaining=8343)
[2026-06-08T09:16:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8372)
[2026-06-08T09:16:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8269)
[2026-06-08T09:16:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8273)
[2026-06-08T09:16:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6423)
[2026-06-08T09:16:31] Searching for fusions with spliced split reads (remaining=6515)
[2026-06-08T09:16:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=3961)
[2026-06-08T09:16:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3934)
[2026-06-08T09:16:38] Searching for fusions with >=4 spliced events (remaining=4602)
[2026-06-08T09:16:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1743)
[2026-06-08T09:16:54] Filtering fusions with anchors <=23nt (remaining=1355)
[2026-06-08T09:16:54] Filtering end-to-end fusions with low support (remaining=1311)
[2026-06-08T09:16:55] Filtering fusions with no coverage around the breakpoints (remaining=1268)
[2026-06-08T09:16:55] Indexing gene sequences 
[2026-06-08T09:17:01] Filtering genes with >=30% identity (remaining=397)
[2026-06-08T09:17:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=119)
[2026-06-08T09:17:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=111)
[2026-06-08T09:17:05] Searching for additional isoforms (remaining=158)
[2026-06-08T09:17:07] Assigning confidence scores to events 
[2026-06-08T09:17:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:17:09] Writing fusions to file '659_bUW-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:17:11] Writing discarded fusions to file '659_bUW-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:17:37] Freeing resources
[2026-06-08T09:17:53] Done (elapsed time=00:11:27, CPU time=00:11:26, peak memory=14.2gb)