[2026-06-08T08:38:18] Launching Arriba 2.4.0
[2026-06-08T08:38:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:33] Reading chimeric alignments from '659_buD-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=8995974)
[2026-06-08T08:43:49] Marking multi-mapping alignments (marked=5384734)
[2026-06-08T08:43:52] Detecting strandedness (reverse)
[2026-06-08T08:43:52] Assigning strands to alignments 
[2026-06-08T08:43:54] Annotating alignments 
[2026-06-08T08:44:19] Filtering duplicates (remaining=5068672)
[2026-06-08T08:44:24] 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=4965270)
[2026-06-08T08:44:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4965270)
[2026-06-08T08:44:27] Filtering viral contigs with expression lower than the top 5 (remaining=4965270)
[2026-06-08T08:44:31] Filtering viral contigs with less than 5% coverage (remaining=4965270)
[2026-06-08T08:44:33] Estimating fragment length (mate gap mean=-90.2458, mate gap stddev=28.1519, read length mean=136.992)
[2026-06-08T08:44:33] Filtering read-through fragments with a distance <=10000bp (remaining=4644914)
[2026-06-08T08:44:35] Filtering inconsistently clipped mates (remaining=4588550)
[2026-06-08T08:44:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4466089)
[2026-06-08T08:44:39] Filtering fragments with small insert size (remaining=4465581)
[2026-06-08T08:44:41] Filtering alignments with long gaps (remaining=4465581)
[2026-06-08T08:44:42] Filtering fragments with both mates in the same gene (remaining=4464918)
[2026-06-08T08:44:44] Filtering fusions arising from hairpin structures (remaining=4274321)
[2026-06-08T08:44:46] Filtering reads with a mismatch p-value <=0.01 (remaining=2177308)
[2026-06-08T08:44:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=794881)
[2026-06-08T08:45:05] Finding fusions and counting supporting reads (total=629249)
[2026-06-08T08:45:18] Merging adjacent fusion breakpoints (remaining=624573)
[2026-06-08T08:45:20] Filtering multi-mapping fusions by alignment score and read support (remaining=394405)
[2026-06-08T08:45:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=392596)
[2026-06-08T08:45:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=198048)
[2026-06-08T08:45:51] Filtering fusions with <2 supporting reads (remaining=28772)
[2026-06-08T08:45:51] Filtering fusions with an e-value >=0.3 (remaining=8734)
[2026-06-08T08:45:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8778)
[2026-06-08T08:45:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8721)
[2026-06-08T08:45:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8721)
[2026-06-08T08:45:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6465)
[2026-06-08T08:46:00] Searching for fusions with spliced split reads (remaining=6593)
[2026-06-08T08:46:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=4159)
[2026-06-08T08:46:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4092)
[2026-06-08T08:46:05] Searching for fusions with >=4 spliced events (remaining=4783)
[2026-06-08T08:46:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1748)
[2026-06-08T08:46:19] Filtering fusions with anchors <=23nt (remaining=1473)
[2026-06-08T08:46:20] Filtering end-to-end fusions with low support (remaining=1435)
[2026-06-08T08:46:20] Filtering fusions with no coverage around the breakpoints (remaining=1386)
[2026-06-08T08:46:21] Indexing gene sequences 
[2026-06-08T08:46:27] Filtering genes with >=30% identity (remaining=443)
[2026-06-08T08:46:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=232)
[2026-06-08T08:46:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=204)
[2026-06-08T08:46:33] Searching for additional isoforms (remaining=253)
[2026-06-08T08:46:34] Assigning confidence scores to events 
[2026-06-08T08:46:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:36] Writing fusions to file '659_buD-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T08:46:38] Writing discarded fusions to file '659_buD-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:59] Freeing resources
[2026-06-08T08:47:14] Done (elapsed time=00:08:56, CPU time=00:08:55, peak memory=13.4gb)