[2026-06-08T08:09:33] Launching Arriba 2.4.0
[2026-06-08T08:09:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:09:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:09:51] Reading chimeric alignments from '659_6i-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=8482615)
[2026-06-08T08:15:07] Marking multi-mapping alignments (marked=5637518)
[2026-06-08T08:15:11] Detecting strandedness (reverse)
[2026-06-08T08:15:11] Assigning strands to alignments 
[2026-06-08T08:15:12] Annotating alignments 
[2026-06-08T08:15:38] Filtering duplicates (remaining=4242313)
[2026-06-08T08:15:43] 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=3987889)
[2026-06-08T08:15:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3987889)
[2026-06-08T08:15:46] Filtering viral contigs with expression lower than the top 5 (remaining=3987889)
[2026-06-08T08:15:49] Filtering viral contigs with less than 5% coverage (remaining=3987889)
[2026-06-08T08:15:51] Estimating fragment length (mate gap mean=-85.1741, mate gap stddev=27.1952, read length mean=121.214)
[2026-06-08T08:15:51] Filtering read-through fragments with a distance <=10000bp (remaining=3802403)
[2026-06-08T08:15:52] Filtering inconsistently clipped mates (remaining=3731527)
[2026-06-08T08:15:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3594073)
[2026-06-08T08:15:57] Filtering fragments with small insert size (remaining=3593046)
[2026-06-08T08:15:58] Filtering alignments with long gaps (remaining=3593046)
[2026-06-08T08:16:00] Filtering fragments with both mates in the same gene (remaining=3592271)
[2026-06-08T08:16:02] Filtering fusions arising from hairpin structures (remaining=3399369)
[2026-06-08T08:16:03] Filtering reads with a mismatch p-value <=0.01 (remaining=1501780)
[2026-06-08T08:16:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=610245)
[2026-06-08T08:16:18] Finding fusions and counting supporting reads (total=477300)
[2026-06-08T08:16:30] Merging adjacent fusion breakpoints (remaining=473364)
[2026-06-08T08:16:31] Filtering multi-mapping fusions by alignment score and read support (remaining=275220)
[2026-06-08T08:16:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:16:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=274200)
[2026-06-08T08:16:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=172277)
[2026-06-08T08:16:59] Filtering fusions with <2 supporting reads (remaining=18267)
[2026-06-08T08:17:00] Filtering fusions with an e-value >=0.3 (remaining=4026)
[2026-06-08T08:17:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4068)
[2026-06-08T08:17:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3995)
[2026-06-08T08:17:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3998)
[2026-06-08T08:17:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3943)
[2026-06-08T08:17:09] Searching for fusions with spliced split reads (remaining=3999)
[2026-06-08T08:17:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=2974)
[2026-06-08T08:17:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2938)
[2026-06-08T08:17:14] Searching for fusions with >=4 spliced events (remaining=3311)
[2026-06-08T08:17:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1077)
[2026-06-08T08:17:28] Filtering fusions with anchors <=23nt (remaining=846)
[2026-06-08T08:17:29] Filtering end-to-end fusions with low support (remaining=816)
[2026-06-08T08:17:29] Filtering fusions with no coverage around the breakpoints (remaining=795)
[2026-06-08T08:17:29] Indexing gene sequences 
[2026-06-08T08:17:33] Filtering genes with >=30% identity (remaining=287)
[2026-06-08T08:17:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=140)
[2026-06-08T08:17:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=132)
[2026-06-08T08:17:37] Searching for additional isoforms (remaining=166)
[2026-06-08T08:17:38] Assigning confidence scores to events 
[2026-06-08T08:17:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:17:40] Writing fusions to file '659_6i-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:17:41] Writing discarded fusions to file '659_6i-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:00] Freeing resources
[2026-06-08T08:18:12] Done (elapsed time=00:08:39, CPU time=00:08:39, peak memory=12.9gb)