[2026-06-04T21:16:48] Launching Arriba 2.4.0
[2026-06-04T21:16:48] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:16:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:16:59] Reading chimeric alignments from '659_Dd-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11376061)
[2026-06-04T21:24:02] Marking multi-mapping alignments (marked=6812124)
[2026-06-04T21:24:06] Detecting strandedness (reverse)
[2026-06-04T21:24:06] Assigning strands to alignments 
[2026-06-04T21:24:09] Annotating alignments 
[2026-06-04T21:24:42] Filtering duplicates (remaining=8212375)
[2026-06-04T21:24:50] 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=7795856)
[2026-06-04T21:24:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7795856)
[2026-06-04T21:24:55] Filtering viral contigs with expression lower than the top 5 (remaining=7795856)
[2026-06-04T21:25:00] Filtering viral contigs with less than 5% coverage (remaining=7795856)
[2026-06-04T21:25:03] Estimating fragment length (mate gap mean=-83.931, mate gap stddev=33.6544, read length mean=136.118)
[2026-06-04T21:25:03] Filtering read-through fragments with a distance <=10000bp (remaining=7397737)
[2026-06-04T21:25:05] Filtering inconsistently clipped mates (remaining=7304286)
[2026-06-04T21:25:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7124760)
[2026-06-04T21:25:12] Filtering fragments with small insert size (remaining=7123695)
[2026-06-04T21:25:14] Filtering alignments with long gaps (remaining=7123693)
[2026-06-04T21:25:17] Filtering fragments with both mates in the same gene (remaining=7122203)
[2026-06-04T21:25:19] Filtering fusions arising from hairpin structures (remaining=6724715)
[2026-06-04T21:25:22] Filtering reads with a mismatch p-value <=0.01 (remaining=3487503)
[2026-06-04T21:25:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=1377485)
[2026-06-04T21:25:51] Finding fusions and counting supporting reads (total=973282)
[2026-06-04T21:26:09] Merging adjacent fusion breakpoints (remaining=965210)
[2026-06-04T21:26:11] Filtering multi-mapping fusions by alignment score and read support (remaining=657774)
[2026-06-04T21:26:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:26:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=654958)
[2026-06-04T21:26:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=387248)
[2026-06-04T21:26:55] Filtering fusions with <2 supporting reads (remaining=54921)
[2026-06-04T21:26:56] Filtering fusions with an e-value >=0.3 (remaining=19717)
[2026-06-04T21:26:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=19778)
[2026-06-04T21:27:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=19596)
[2026-06-04T21:27:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=19625)
[2026-06-04T21:27:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=11773)
[2026-06-04T21:27:10] Searching for fusions with spliced split reads (remaining=11826)
[2026-06-04T21:27:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=5527)
[2026-06-04T21:27:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5473)
[2026-06-04T21:27:19] Searching for fusions with >=4 spliced events (remaining=6722)
[2026-06-04T21:27:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2442)
[2026-06-04T21:27:40] Filtering fusions with anchors <=23nt (remaining=1639)
[2026-06-04T21:27:41] Filtering end-to-end fusions with low support (remaining=1601)
[2026-06-04T21:27:41] Filtering fusions with no coverage around the breakpoints (remaining=1574)
[2026-06-04T21:27:42] Indexing gene sequences 
[2026-06-04T21:27:48] Filtering genes with >=30% identity (remaining=475)
[2026-06-04T21:27:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=223)
[2026-06-04T21:27:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=194)
[2026-06-04T21:27:59] Searching for additional isoforms (remaining=251)
[2026-06-04T21:28:00] Assigning confidence scores to events 
[2026-06-04T21:28:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:28:04] Writing fusions to file '659_Dd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:28:07] Writing discarded fusions to file '659_Dd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:28:38] Freeing resources
[2026-06-04T21:28:57] Done (elapsed time=00:12:09, CPU time=00:12:08, peak memory=16.1gb)