[2026-06-04T20:42:38] Launching Arriba 2.4.0
[2026-06-04T20:42:38] Loading assembly from 'ref_genome.fa' 
[2026-06-04T20:42:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T20:42:49] Reading chimeric alignments from '659_ri-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=6662546)
[2026-06-04T20:46:17] Marking multi-mapping alignments (marked=4550521)
[2026-06-04T20:46:19] Detecting strandedness (reverse)
[2026-06-04T20:46:19] Assigning strands to alignments 
[2026-06-04T20:46:20] Annotating alignments 
[2026-06-04T20:46:40] Filtering duplicates (remaining=4062956)
[2026-06-04T20:46:44] 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=3712172)
[2026-06-04T20:46:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3712172)
[2026-06-04T20:46:47] Filtering viral contigs with expression lower than the top 5 (remaining=3712172)
[2026-06-04T20:46:49] Filtering viral contigs with less than 5% coverage (remaining=3712172)
[2026-06-04T20:46:51] Estimating fragment length (mate gap mean=-79.7017, mate gap stddev=27.4656, read length mean=115.19)
[2026-06-04T20:46:51] Filtering read-through fragments with a distance <=10000bp (remaining=3531897)
[2026-06-04T20:46:53] Filtering inconsistently clipped mates (remaining=3485643)
[2026-06-04T20:46:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3346454)
[2026-06-04T20:46:56] Filtering fragments with small insert size (remaining=3345559)
[2026-06-04T20:46:57] Filtering alignments with long gaps (remaining=3345559)
[2026-06-04T20:46:59] Filtering fragments with both mates in the same gene (remaining=3344769)
[2026-06-04T20:47:00] Filtering fusions arising from hairpin structures (remaining=3238780)
[2026-06-04T20:47:02] Filtering reads with a mismatch p-value <=0.01 (remaining=1494251)
[2026-06-04T20:47:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=518534)
[2026-06-04T20:47:15] Finding fusions and counting supporting reads (total=403061)
[2026-06-04T20:47:25] Merging adjacent fusion breakpoints (remaining=400108)
[2026-06-04T20:47:26] Filtering multi-mapping fusions by alignment score and read support (remaining=224820)
[2026-06-04T20:47:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T20:47:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=224220)
[2026-06-04T20:47:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=152984)
[2026-06-04T20:47:50] Filtering fusions with <2 supporting reads (remaining=15662)
[2026-06-04T20:47:50] Filtering fusions with an e-value >=0.3 (remaining=3519)
[2026-06-04T20:47:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3546)
[2026-06-04T20:47:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3500)
[2026-06-04T20:47:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3502)
[2026-06-04T20:47:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3494)
[2026-06-04T20:47:57] Searching for fusions with spliced split reads (remaining=3628)
[2026-06-04T20:48:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=2633)
[2026-06-04T20:48:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2618)
[2026-06-04T20:48:02] Searching for fusions with >=4 spliced events (remaining=2850)
[2026-06-04T20:48:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1080)
[2026-06-04T20:48:14] Filtering fusions with anchors <=23nt (remaining=790)
[2026-06-04T20:48:15] Filtering end-to-end fusions with low support (remaining=771)
[2026-06-04T20:48:15] Filtering fusions with no coverage around the breakpoints (remaining=750)
[2026-06-04T20:48:16] Indexing gene sequences 
[2026-06-04T20:48:19] Filtering genes with >=30% identity (remaining=271)
[2026-06-04T20:48:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=104)
[2026-06-04T20:48:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=100)
[2026-06-04T20:48:23] Searching for additional isoforms (remaining=123)
[2026-06-04T20:48:23] Assigning confidence scores to events 
[2026-06-04T20:48:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T20:48:26] Writing fusions to file '659_ri-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T20:48:26] Writing discarded fusions to file '659_ri-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T20:48:44] Freeing resources
[2026-06-04T20:48:54] Done (elapsed time=00:06:16, CPU time=00:06:15, peak memory=11gb)