[2026-06-08T09:10:21] Launching Arriba 2.4.0
[2026-06-08T09:10:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:10:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:10:40] Reading chimeric alignments from '659_c95-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9863692)
[2026-06-08T09:18:49] Marking multi-mapping alignments (marked=6206604)
[2026-06-08T09:18:53] Detecting strandedness (reverse)
[2026-06-08T09:18:53] Assigning strands to alignments 
[2026-06-08T09:18:55] Annotating alignments 
[2026-06-08T09:19:25] Filtering duplicates (remaining=4961358)
[2026-06-08T09:19:30] 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=4774205)
[2026-06-08T09:19:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4774205)
[2026-06-08T09:19:33] Filtering viral contigs with expression lower than the top 5 (remaining=4774205)
[2026-06-08T09:19:37] Filtering viral contigs with less than 5% coverage (remaining=4774205)
[2026-06-08T09:19:39] Estimating fragment length (mate gap mean=-87.0509, mate gap stddev=29.8423, read length mean=134.212)
[2026-06-08T09:19:39] Filtering read-through fragments with a distance <=10000bp (remaining=4455306)
[2026-06-08T09:19:41] Filtering inconsistently clipped mates (remaining=4385959)
[2026-06-08T09:19:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4249958)
[2026-06-08T09:19:46] Filtering fragments with small insert size (remaining=4249402)
[2026-06-08T09:19:48] Filtering alignments with long gaps (remaining=4249400)
[2026-06-08T09:19:50] Filtering fragments with both mates in the same gene (remaining=4248564)
[2026-06-08T09:19:51] Filtering fusions arising from hairpin structures (remaining=4008236)
[2026-06-08T09:19:53] Filtering reads with a mismatch p-value <=0.01 (remaining=1806678)
[2026-06-08T09:20:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=804112)
[2026-06-08T09:20:13] Finding fusions and counting supporting reads (total=633251)
[2026-06-08T09:20:27] Merging adjacent fusion breakpoints (remaining=624432)
[2026-06-08T09:20:28] Filtering multi-mapping fusions by alignment score and read support (remaining=389420)
[2026-06-08T09:20:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:21:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=386313)
[2026-06-08T09:21:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=192354)
[2026-06-08T09:21:01] Filtering fusions with <2 supporting reads (remaining=29689)
[2026-06-08T09:21:02] Filtering fusions with an e-value >=0.3 (remaining=10472)
[2026-06-08T09:21:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10535)
[2026-06-08T09:21:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10395)
[2026-06-08T09:21:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10395)
[2026-06-08T09:21:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6574)
[2026-06-08T09:21:11] Searching for fusions with spliced split reads (remaining=6726)
[2026-06-08T09:21:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=4258)
[2026-06-08T09:21:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4179)
[2026-06-08T09:21:17] Searching for fusions with >=4 spliced events (remaining=4892)
[2026-06-08T09:21:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1878)
[2026-06-08T09:21:41] Filtering fusions with anchors <=23nt (remaining=1432)
[2026-06-08T09:21:41] Filtering end-to-end fusions with low support (remaining=1388)
[2026-06-08T09:21:42] Filtering fusions with no coverage around the breakpoints (remaining=1354)
[2026-06-08T09:21:42] Indexing gene sequences 
[2026-06-08T09:21:48] Filtering genes with >=30% identity (remaining=536)
[2026-06-08T09:21:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=285)
[2026-06-08T09:21:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=223)
[2026-06-08T09:21:56] Searching for additional isoforms (remaining=309)
[2026-06-08T09:21:57] Assigning confidence scores to events 
[2026-06-08T09:22:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:22:00] Writing fusions to file '659_c95-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:22:03] Writing discarded fusions to file '659_c95-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:22:26] Freeing resources
[2026-06-08T09:22:42] Done (elapsed time=00:12:21, CPU time=00:12:20, peak memory=14.5gb)