[2026-06-08T08:33:20] Launching Arriba 2.4.0
[2026-06-08T08:33:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:33:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:33:39] Reading chimeric alignments from '659_bhK-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10912946)
[2026-06-08T08:43:51] Marking multi-mapping alignments (marked=6636644)
[2026-06-08T08:43:55] Detecting strandedness (reverse)
[2026-06-08T08:43:55] Assigning strands to alignments 
[2026-06-08T08:43:57] Annotating alignments 
[2026-06-08T08:44:33] Filtering duplicates (remaining=7269437)
[2026-06-08T08:44:41] 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=6830043)
[2026-06-08T08:44:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6830043)
[2026-06-08T08:44:46] Filtering viral contigs with expression lower than the top 5 (remaining=6830043)
[2026-06-08T08:44:52] Filtering viral contigs with less than 5% coverage (remaining=6830043)
[2026-06-08T08:44:54] Estimating fragment length (mate gap mean=-85.7017, mate gap stddev=30.0068, read length mean=132.736)
[2026-06-08T08:44:54] Filtering read-through fragments with a distance <=10000bp (remaining=6485069)
[2026-06-08T08:44:57] Filtering inconsistently clipped mates (remaining=6347897)
[2026-06-08T08:44:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6207789)
[2026-06-08T08:45:04] Filtering fragments with small insert size (remaining=6206252)
[2026-06-08T08:45:07] Filtering alignments with long gaps (remaining=6206252)
[2026-06-08T08:45:09] Filtering fragments with both mates in the same gene (remaining=6205158)
[2026-06-08T08:45:12] Filtering fusions arising from hairpin structures (remaining=5691885)
[2026-06-08T08:45:15] Filtering reads with a mismatch p-value <=0.01 (remaining=2944049)
[2026-06-08T08:45:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=1218981)
[2026-06-08T08:45:46] Finding fusions and counting supporting reads (total=883805)
[2026-06-08T08:46:05] Merging adjacent fusion breakpoints (remaining=874095)
[2026-06-08T08:46:06] Filtering multi-mapping fusions by alignment score and read support (remaining=567150)
[2026-06-08T08:46:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=565058)
[2026-06-08T08:46:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=351308)
[2026-06-08T08:46:56] Filtering fusions with <2 supporting reads (remaining=44206)
[2026-06-08T08:46:57] Filtering fusions with an e-value >=0.3 (remaining=11015)
[2026-06-08T08:46:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11106)
[2026-06-08T08:47:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10990)
[2026-06-08T08:47:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10994)
[2026-06-08T08:47:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7663)
[2026-06-08T08:47:08] Searching for fusions with spliced split reads (remaining=7787)
[2026-06-08T08:47:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=4716)
[2026-06-08T08:47:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4666)
[2026-06-08T08:47:16] Searching for fusions with >=4 spliced events (remaining=5420)
[2026-06-08T08:47:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1661)
[2026-06-08T08:47:37] Filtering fusions with anchors <=23nt (remaining=1270)
[2026-06-08T08:47:38] Filtering end-to-end fusions with low support (remaining=1250)
[2026-06-08T08:47:39] Filtering fusions with no coverage around the breakpoints (remaining=1226)
[2026-06-08T08:47:40] Indexing gene sequences 
[2026-06-08T08:47:46] Filtering genes with >=30% identity (remaining=385)
[2026-06-08T08:47:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=198)
[2026-06-08T08:47:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-08T08:47:53] Searching for additional isoforms (remaining=223)
[2026-06-08T08:47:55] Assigning confidence scores to events 
[2026-06-08T08:47:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:58] Writing fusions to file '659_bhK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:00] Writing discarded fusions to file '659_bhK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:36] Freeing resources
[2026-06-08T08:48:53] Done (elapsed time=00:15:33, CPU time=00:15:33, peak memory=15.5gb)