[2026-06-08T08:22:44] Launching Arriba 2.4.0
[2026-06-08T08:22:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:22:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:22:57] Reading chimeric alignments from '659_dRe-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=8515474)
[2026-06-08T08:29:18] Marking multi-mapping alignments (marked=5351491)
[2026-06-08T08:29:21] Detecting strandedness (reverse)
[2026-06-08T08:29:21] Assigning strands to alignments 
[2026-06-08T08:29:23] Annotating alignments 
[2026-06-08T08:29:49] Filtering duplicates (remaining=5858220)
[2026-06-08T08:29:55] 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)
[2026-06-08T08:29:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5640829)
[2026-06-08T08:29:58] Filtering viral contigs with expression lower than the top 5 (remaining=5640829)
[2026-06-08T08:30:02] Filtering viral contigs with less than 5% coverage (remaining=5640829)
[2026-06-08T08:30:04] Estimating fragment length (mate gap mean=-86.8442, mate gap stddev=29.0112, read length mean=133.488)
[2026-06-08T08:30:04] Filtering read-through fragments with a distance <=10000bp (remaining=5172246)
[2026-06-08T08:30:06] Filtering inconsistently clipped mates (remaining=5101729)
[2026-06-08T08:30:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4929015)
[2026-06-08T08:30:12] Filtering fragments with small insert size (remaining=4928468)
[2026-06-08T08:30:13] Filtering alignments with long gaps (remaining=4928468)
[2026-06-08T08:30:15] Filtering fragments with both mates in the same gene (remaining=4927633)
[2026-06-08T08:30:17] Filtering fusions arising from hairpin structures (remaining=4651458)
[2026-06-08T08:30:20] Filtering reads with a mismatch p-value <=0.01 (remaining=2497276)
[2026-06-08T08:30:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=1118609)
[2026-06-08T08:30:41] Finding fusions and counting supporting reads (total=725150)
[2026-06-08T08:30:54] Merging adjacent fusion breakpoints (remaining=713692)
[2026-06-08T08:30:56] Filtering multi-mapping fusions by alignment score and read support (remaining=450611)
[2026-06-08T08:31:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:31:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=448823)
[2026-06-08T08:31:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=238406)
[2026-06-08T08:31:31] Filtering fusions with <2 supporting reads (remaining=38472)
[2026-06-08T08:31:31] Filtering fusions with an e-value >=0.3 (remaining=14032)
[2026-06-08T08:31:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14093)
[2026-06-08T08:31:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14011)
[2026-06-08T08:31:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14012)
[2026-06-08T08:31:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8306)
[2026-06-08T08:31:41] Searching for fusions with spliced split reads (remaining=8324)
[2026-06-08T08:31:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=4556)
[2026-06-08T08:31:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4498)
[2026-06-08T08:31:47] Searching for fusions with >=4 spliced events (remaining=5316)
[2026-06-08T08:31:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1985)
[2026-06-08T08:32:01] Filtering fusions with anchors <=23nt (remaining=1597)
[2026-06-08T08:32:02] Filtering end-to-end fusions with low support (remaining=1545)
[2026-06-08T08:32:02] Filtering fusions with no coverage around the breakpoints (remaining=1485)
[2026-06-08T08:32:03] Indexing gene sequences 
[2026-06-08T08:32:09] Filtering genes with >=30% identity (remaining=489)
[2026-06-08T08:32:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=234)
[2026-06-08T08:32:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=207)
[2026-06-08T08:32:37] Searching for additional isoforms (remaining=305)
[2026-06-08T08:32:38] Assigning confidence scores to events 
[2026-06-08T08:32:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:41] Writing fusions to file '659_dRe-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:32:43] Writing discarded fusions to file '659_dRe-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:33:08] Freeing resources
[2026-06-08T08:33:23] Done (elapsed time=00:10:39, CPU time=00:10:38, peak memory=13.1gb)