[2026-06-08T08:30:54] Launching Arriba 2.4.0
[2026-06-08T08:30:54] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:06] Reading chimeric alignments from '659_Fr-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9749883)
[2026-06-08T08:37:38] Marking multi-mapping alignments (marked=6252794)
[2026-06-08T08:37:41] Detecting strandedness (reverse)
[2026-06-08T08:37:41] Assigning strands to alignments 
[2026-06-08T08:37:43] Annotating alignments 
[2026-06-08T08:38:13] Filtering duplicates (remaining=5693445)
[2026-06-08T08:38:18] 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=5445408)
[2026-06-08T08:38:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5445408)
[2026-06-08T08:38:22] Filtering viral contigs with expression lower than the top 5 (remaining=5445408)
[2026-06-08T08:38:26] Filtering viral contigs with less than 5% coverage (remaining=5445408)
[2026-06-08T08:38:28] Estimating fragment length (mate gap mean=-89.2115, mate gap stddev=28.2917, read length mean=131.621)
[2026-06-08T08:38:28] Filtering read-through fragments with a distance <=10000bp (remaining=5117512)
[2026-06-08T08:38:30] Filtering inconsistently clipped mates (remaining=5012504)
[2026-06-08T08:38:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4867937)
[2026-06-08T08:38:35] Filtering fragments with small insert size (remaining=4867207)
[2026-06-08T08:38:37] Filtering alignments with long gaps (remaining=4867207)
[2026-06-08T08:38:38] Filtering fragments with both mates in the same gene (remaining=4866200)
[2026-06-08T08:38:40] Filtering fusions arising from hairpin structures (remaining=4499041)
[2026-06-08T08:38:43] Filtering reads with a mismatch p-value <=0.01 (remaining=2250387)
[2026-06-08T08:38:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=909652)
[2026-06-08T08:39:03] Finding fusions and counting supporting reads (total=642665)
[2026-06-08T08:39:17] Merging adjacent fusion breakpoints (remaining=633122)
[2026-06-08T08:39:18] Filtering multi-mapping fusions by alignment score and read support (remaining=402896)
[2026-06-08T08:39:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=400835)
[2026-06-08T08:39:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=205198)
[2026-06-08T08:39:54] Filtering fusions with <2 supporting reads (remaining=27504)
[2026-06-08T08:39:55] Filtering fusions with an e-value >=0.3 (remaining=7147)
[2026-06-08T08:39:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7195)
[2026-06-08T08:39:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7106)
[2026-06-08T08:39:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7106)
[2026-06-08T08:40:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6226)
[2026-06-08T08:40:05] Searching for fusions with spliced split reads (remaining=6358)
[2026-06-08T08:40:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=4173)
[2026-06-08T08:40:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4118)
[2026-06-08T08:40:11] Searching for fusions with >=4 spliced events (remaining=4929)
[2026-06-08T08:40:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1837)
[2026-06-08T08:40:24] Filtering fusions with anchors <=23nt (remaining=1485)
[2026-06-08T08:40:25] Filtering end-to-end fusions with low support (remaining=1443)
[2026-06-08T08:40:26] Filtering fusions with no coverage around the breakpoints (remaining=1415)
[2026-06-08T08:40:26] Indexing gene sequences 
[2026-06-08T08:40:32] Filtering genes with >=30% identity (remaining=523)
[2026-06-08T08:40:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=278)
[2026-06-08T08:40:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=219)
[2026-06-08T08:40:47] Searching for additional isoforms (remaining=296)
[2026-06-08T08:40:48] Assigning confidence scores to events 
[2026-06-08T08:40:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:51] Writing fusions to file '659_Fr-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:40:53] Writing discarded fusions to file '659_Fr-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:18] Freeing resources
[2026-06-08T08:41:32] Done (elapsed time=00:10:38, CPU time=00:10:38, peak memory=14.4gb)