[2026-06-08T09:05:37] Launching Arriba 2.4.0
[2026-06-08T09:05:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:05:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:05:54] Reading chimeric alignments from '659_cRa-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11486785)
[2026-06-08T09:14:23] Marking multi-mapping alignments (marked=6864890)
[2026-06-08T09:14:27] Detecting strandedness (reverse)
[2026-06-08T09:14:27] Assigning strands to alignments 
[2026-06-08T09:14:29] Annotating alignments 
[2026-06-08T09:15:02] Filtering duplicates (remaining=5748078)
[2026-06-08T09:15:09] 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=5608118)
[2026-06-08T09:15:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5608118)
[2026-06-08T09:15:13] Filtering viral contigs with expression lower than the top 5 (remaining=5608118)
[2026-06-08T09:15:17] Filtering viral contigs with less than 5% coverage (remaining=5608118)
[2026-06-08T09:15:20] Estimating fragment length (mate gap mean=-89.7221, mate gap stddev=29.3924, read length mean=140.116)
[2026-06-08T09:15:20] Filtering read-through fragments with a distance <=10000bp (remaining=5312472)
[2026-06-08T09:15:22] Filtering inconsistently clipped mates (remaining=5244444)
[2026-06-08T09:15:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5073254)
[2026-06-08T09:15:28] Filtering fragments with small insert size (remaining=5072463)
[2026-06-08T09:15:30] Filtering alignments with long gaps (remaining=5072459)
[2026-06-08T09:15:32] Filtering fragments with both mates in the same gene (remaining=5071681)
[2026-06-08T09:15:34] Filtering fusions arising from hairpin structures (remaining=4830213)
[2026-06-08T09:15:36] Filtering reads with a mismatch p-value <=0.01 (remaining=2342067)
[2026-06-08T09:15:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=765340)
[2026-06-08T09:15:59] Finding fusions and counting supporting reads (total=594161)
[2026-06-08T09:16:15] Merging adjacent fusion breakpoints (remaining=588412)
[2026-06-08T09:16:16] Filtering multi-mapping fusions by alignment score and read support (remaining=380628)
[2026-06-08T09:16:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:16:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=377865)
[2026-06-08T09:16:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=193285)
[2026-06-08T09:16:54] Filtering fusions with <2 supporting reads (remaining=31060)
[2026-06-08T09:16:55] Filtering fusions with an e-value >=0.3 (remaining=11007)
[2026-06-08T09:16:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11062)
[2026-06-08T09:16:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10960)
[2026-06-08T09:16:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10960)
[2026-06-08T09:17:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5926)
[2026-06-08T09:17:05] Searching for fusions with spliced split reads (remaining=6081)
[2026-06-08T09:17:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=3876)
[2026-06-08T09:17:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3835)
[2026-06-08T09:17:11] Searching for fusions with >=4 spliced events (remaining=4570)
[2026-06-08T09:17:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1606)
[2026-06-08T09:17:26] Filtering fusions with anchors <=23nt (remaining=1264)
[2026-06-08T09:17:27] Filtering end-to-end fusions with low support (remaining=1226)
[2026-06-08T09:17:27] Filtering fusions with no coverage around the breakpoints (remaining=1200)
[2026-06-08T09:17:28] Indexing gene sequences 
[2026-06-08T09:17:33] Filtering genes with >=30% identity (remaining=400)
[2026-06-08T09:17:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=209)
[2026-06-08T09:17:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=177)
[2026-06-08T09:17:38] Searching for additional isoforms (remaining=226)
[2026-06-08T09:17:39] Assigning confidence scores to events 
[2026-06-08T09:17:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:17:42] Writing fusions to file '659_cRa-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:17:43] Writing discarded fusions to file '659_cRa-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:18:05] Freeing resources
[2026-06-08T09:18:24] Done (elapsed time=00:12:47, CPU time=00:12:46, peak memory=15.7gb)