[2026-06-04T21:13:44] Launching Arriba 2.4.0
[2026-06-04T21:13:44] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:13:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:13:56] Reading chimeric alignments from '659_end-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=8534011)
[2026-06-04T21:20:38] Marking multi-mapping alignments (marked=4914116)
[2026-06-04T21:20:41] Detecting strandedness (reverse)
[2026-06-04T21:20:41] Assigning strands to alignments 
[2026-06-04T21:20:43] Annotating alignments 
[2026-06-04T21:21:15] Filtering duplicates (remaining=6225050)
[2026-06-04T21:21:23] 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=5977201)
[2026-06-04T21:21:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5977201)
[2026-06-04T21:21:26] Filtering viral contigs with expression lower than the top 5 (remaining=5977201)
[2026-06-04T21:21:31] Filtering viral contigs with less than 5% coverage (remaining=5977201)
[2026-06-04T21:21:33] Estimating fragment length (mate gap mean=-87.5229, mate gap stddev=29.8551, read length mean=135.247)
[2026-06-04T21:21:33] Filtering read-through fragments with a distance <=10000bp (remaining=5580335)
[2026-06-04T21:21:35] Filtering inconsistently clipped mates (remaining=5512817)
[2026-06-04T21:21:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5354623)
[2026-06-04T21:21:40] Filtering fragments with small insert size (remaining=5354061)
[2026-06-04T21:21:42] Filtering alignments with long gaps (remaining=5354061)
[2026-06-04T21:21:44] Filtering fragments with both mates in the same gene (remaining=5352905)
[2026-06-04T21:21:45] Filtering fusions arising from hairpin structures (remaining=5133966)
[2026-06-04T21:21:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2855058)
[2026-06-04T21:22:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=1281584)
[2026-06-04T21:22:13] Finding fusions and counting supporting reads (total=848462)
[2026-06-04T21:22:28] Merging adjacent fusion breakpoints (remaining=840752)
[2026-06-04T21:22:30] Filtering multi-mapping fusions by alignment score and read support (remaining=562770)
[2026-06-04T21:22:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:23:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=560447)
[2026-06-04T21:23:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=319789)
[2026-06-04T21:23:08] Filtering fusions with <2 supporting reads (remaining=46937)
[2026-06-04T21:23:09] Filtering fusions with an e-value >=0.3 (remaining=13420)
[2026-06-04T21:23:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13470)
[2026-06-04T21:23:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13361)
[2026-06-04T21:23:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13361)
[2026-06-04T21:23:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8999)
[2026-06-04T21:23:19] Searching for fusions with spliced split reads (remaining=9049)
[2026-06-04T21:23:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=5248)
[2026-06-04T21:23:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5186)
[2026-06-04T21:23:26] Searching for fusions with >=4 spliced events (remaining=6389)
[2026-06-04T21:23:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2356)
[2026-06-04T21:23:41] Filtering fusions with anchors <=23nt (remaining=1912)
[2026-06-04T21:23:42] Filtering end-to-end fusions with low support (remaining=1866)
[2026-06-04T21:23:42] Filtering fusions with no coverage around the breakpoints (remaining=1820)
[2026-06-04T21:23:43] Indexing gene sequences 
[2026-06-04T21:23:50] Filtering genes with >=30% identity (remaining=612)
[2026-06-04T21:23:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=328)
[2026-06-04T21:24:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=224)
[2026-06-04T21:24:13] Searching for additional isoforms (remaining=351)
[2026-06-04T21:24:15] Assigning confidence scores to events 
[2026-06-04T21:24:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:24:18] Writing fusions to file '659_end-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:24:21] Writing discarded fusions to file '659_end-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:24:51] Freeing resources
[2026-06-04T21:25:07] Done (elapsed time=00:11:23, CPU time=00:11:22, peak memory=13gb)