[2026-06-04T21:12:43] Launching Arriba 2.4.0
[2026-06-04T21:12:43] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:12:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:12:55] Reading chimeric alignments from '659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=8198121)
[2026-06-04T21:19:15] Marking multi-mapping alignments (marked=4751958)
[2026-06-04T21:19:18] Detecting strandedness (reverse)
[2026-06-04T21:19:18] Assigning strands to alignments 
[2026-06-04T21:19:20] Annotating alignments 
[2026-06-04T21:19:44] Filtering duplicates (remaining=5595811)
[2026-06-04T21:19:49] 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=5379273)
[2026-06-04T21:19:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5379273)
[2026-06-04T21:19:52] Filtering viral contigs with expression lower than the top 5 (remaining=5379273)
[2026-06-04T21:19:56] Filtering viral contigs with less than 5% coverage (remaining=5379273)
[2026-06-04T21:19:58] Estimating fragment length (mate gap mean=-86.6452, mate gap stddev=29.228, read length mean=133.393)
[2026-06-04T21:19:58] Filtering read-through fragments with a distance <=10000bp (remaining=5058781)
[2026-06-04T21:20:00] Filtering inconsistently clipped mates (remaining=4978934)
[2026-06-04T21:20:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4848220)
[2026-06-04T21:20:05] Filtering fragments with small insert size (remaining=4847451)
[2026-06-04T21:20:06] Filtering alignments with long gaps (remaining=4847451)
[2026-06-04T21:20:08] Filtering fragments with both mates in the same gene (remaining=4846462)
[2026-06-04T21:20:10] Filtering fusions arising from hairpin structures (remaining=4573372)
[2026-06-04T21:20:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2465491)
[2026-06-04T21:20:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=1001867)
[2026-06-04T21:20:32] Finding fusions and counting supporting reads (total=694945)
[2026-06-04T21:20:45] Merging adjacent fusion breakpoints (remaining=685951)
[2026-06-04T21:20:46] Filtering multi-mapping fusions by alignment score and read support (remaining=489160)
[2026-06-04T21:21:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:21:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=487751)
[2026-06-04T21:21:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=243562)
[2026-06-04T21:21:17] Filtering fusions with <2 supporting reads (remaining=38806)
[2026-06-04T21:21:18] Filtering fusions with an e-value >=0.3 (remaining=12117)
[2026-06-04T21:21:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12173)
[2026-06-04T21:21:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12076)
[2026-06-04T21:21:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12076)
[2026-06-04T21:21:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7036)
[2026-06-04T21:21:27] Searching for fusions with spliced split reads (remaining=7153)
[2026-06-04T21:21:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=4351)
[2026-06-04T21:21:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4322)
[2026-06-04T21:21:33] Searching for fusions with >=4 spliced events (remaining=5131)
[2026-06-04T21:21:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1798)
[2026-06-04T21:21:47] Filtering fusions with anchors <=23nt (remaining=1412)
[2026-06-04T21:21:47] Filtering end-to-end fusions with low support (remaining=1384)
[2026-06-04T21:21:48] Filtering fusions with no coverage around the breakpoints (remaining=1358)
[2026-06-04T21:21:48] Indexing gene sequences 
[2026-06-04T21:21:53] Filtering genes with >=30% identity (remaining=454)
[2026-06-04T21:21:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=233)
[2026-06-04T21:22:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=207)
[2026-06-04T21:22:03] Searching for additional isoforms (remaining=265)
[2026-06-04T21:22:04] Assigning confidence scores to events 
[2026-06-04T21:22:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:22:06] Writing fusions to file '659_bTo-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:22:08] Writing discarded fusions to file '659_bTo-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:22:30] Freeing resources
[2026-06-04T21:22:45] Done (elapsed time=00:10:02, CPU time=00:10:00, peak memory=12.7gb)