[2026-06-04T21:08:46] Launching Arriba 2.4.0
[2026-06-04T21:08:46] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:08:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:08:57] Reading chimeric alignments from '659_dRe-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=8515474)
[2026-06-04T21:15:05] Marking multi-mapping alignments (marked=5351491)
[2026-06-04T21:15:09] Detecting strandedness (reverse)
[2026-06-04T21:15:09] Assigning strands to alignments 
[2026-06-04T21:15:10] Annotating alignments 
[2026-06-04T21:15:34] Filtering duplicates (remaining=5858220)
[2026-06-04T21:15:39] 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=5640829)
[2026-06-04T21:15:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5640829)
[2026-06-04T21:15:43] Filtering viral contigs with expression lower than the top 5 (remaining=5640829)
[2026-06-04T21:15:46] Filtering viral contigs with less than 5% coverage (remaining=5640829)
[2026-06-04T21:15:48] Estimating fragment length (mate gap mean=-86.8442, mate gap stddev=29.0112, read length mean=133.488)
[2026-06-04T21:15:48] Filtering read-through fragments with a distance <=10000bp (remaining=5172246)
[2026-06-04T21:15:50] Filtering inconsistently clipped mates (remaining=5101729)
[2026-06-04T21:15:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4929015)
[2026-06-04T21:15:55] Filtering fragments with small insert size (remaining=4928468)
[2026-06-04T21:15:57] Filtering alignments with long gaps (remaining=4928468)
[2026-06-04T21:15:58] Filtering fragments with both mates in the same gene (remaining=4927633)
[2026-06-04T21:16:00] Filtering fusions arising from hairpin structures (remaining=4651458)
[2026-06-04T21:16:02] Filtering reads with a mismatch p-value <=0.01 (remaining=2497276)
[2026-06-04T21:16:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=1118609)
[2026-06-04T21:16:22] Finding fusions and counting supporting reads (total=725150)
[2026-06-04T21:16:34] Merging adjacent fusion breakpoints (remaining=713692)
[2026-06-04T21:16:36] Filtering multi-mapping fusions by alignment score and read support (remaining=450611)
[2026-06-04T21:17:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:17:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=448823)
[2026-06-04T21:17:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=238406)
[2026-06-04T21:17:07] Filtering fusions with <2 supporting reads (remaining=38472)
[2026-06-04T21:17:07] Filtering fusions with an e-value >=0.3 (remaining=14032)
[2026-06-04T21:17:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14093)
[2026-06-04T21:17:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14011)
[2026-06-04T21:17:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14012)
[2026-06-04T21:17:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8306)
[2026-06-04T21:17:17] Searching for fusions with spliced split reads (remaining=8324)
[2026-06-04T21:17:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4556)
[2026-06-04T21:17:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4498)
[2026-06-04T21:17:22] Searching for fusions with >=4 spliced events (remaining=5316)
[2026-06-04T21:17:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1985)
[2026-06-04T21:17:36] Filtering fusions with anchors <=23nt (remaining=1597)
[2026-06-04T21:17:37] Filtering end-to-end fusions with low support (remaining=1545)
[2026-06-04T21:17:37] Filtering fusions with no coverage around the breakpoints (remaining=1485)
[2026-06-04T21:17:38] Indexing gene sequences 
[2026-06-04T21:17:44] Filtering genes with >=30% identity (remaining=489)
[2026-06-04T21:17:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=234)
[2026-06-04T21:18:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=207)
[2026-06-04T21:18:11] Searching for additional isoforms (remaining=305)
[2026-06-04T21:18:12] Assigning confidence scores to events 
[2026-06-04T21:18:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:18:15] Writing fusions to file '659_dRe-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:18:17] Writing discarded fusions to file '659_dRe-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:18:39] Freeing resources
[2026-06-04T21:18:53] Done (elapsed time=00:10:07, CPU time=00:10:06, peak memory=13.1gb)