[2026-06-08T07:58:25] Launching Arriba 2.4.0
[2026-06-08T07:58:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:58:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:58:46] Reading chimeric alignments from '659_ri-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=6662546)
[2026-06-08T08:03:56] Marking multi-mapping alignments (marked=4550521)
[2026-06-08T08:03:59] Detecting strandedness (reverse)
[2026-06-08T08:03:59] Assigning strands to alignments 
[2026-06-08T08:04:00] Annotating alignments 
[2026-06-08T08:04:26] Filtering duplicates (remaining=4062956)
[2026-06-08T08:04:33] 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)
[2026-06-08T08:04:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3712172)
[2026-06-08T08:04:35] Filtering viral contigs with expression lower than the top 5 (remaining=3712172)
[2026-06-08T08:04:38] Filtering viral contigs with less than 5% coverage (remaining=3712172)
[2026-06-08T08:04:40] Estimating fragment length (mate gap mean=-79.7017, mate gap stddev=27.4656, read length mean=115.19)
[2026-06-08T08:04:40] Filtering read-through fragments with a distance <=10000bp (remaining=3531897)
[2026-06-08T08:04:41] Filtering inconsistently clipped mates (remaining=3485643)
[2026-06-08T08:04:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3346454)
[2026-06-08T08:04:45] Filtering fragments with small insert size (remaining=3345559)
[2026-06-08T08:04:47] Filtering alignments with long gaps (remaining=3345559)
[2026-06-08T08:04:48] Filtering fragments with both mates in the same gene (remaining=3344769)
[2026-06-08T08:04:49] Filtering fusions arising from hairpin structures (remaining=3238780)
[2026-06-08T08:04:51] Filtering reads with a mismatch p-value <=0.01 (remaining=1494251)
[2026-06-08T08:05:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=518534)
[2026-06-08T08:05:07] Finding fusions and counting supporting reads (total=403061)
[2026-06-08T08:05:19] Merging adjacent fusion breakpoints (remaining=400108)
[2026-06-08T08:05:20] Filtering multi-mapping fusions by alignment score and read support (remaining=224820)
[2026-06-08T08:05:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:05:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=224220)
[2026-06-08T08:05:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=152984)
[2026-06-08T08:05:50] Filtering fusions with <2 supporting reads (remaining=15662)
[2026-06-08T08:05:51] Filtering fusions with an e-value >=0.3 (remaining=3519)
[2026-06-08T08:05:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3546)
[2026-06-08T08:05:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3500)
[2026-06-08T08:05:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3502)
[2026-06-08T08:05:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3494)
[2026-06-08T08:05:58] Searching for fusions with spliced split reads (remaining=3628)
[2026-06-08T08:06:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=2633)
[2026-06-08T08:06:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2618)
[2026-06-08T08:06:04] Searching for fusions with >=4 spliced events (remaining=2850)
[2026-06-08T08:06:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1080)
[2026-06-08T08:06:21] Filtering fusions with anchors <=23nt (remaining=790)
[2026-06-08T08:06:22] Filtering end-to-end fusions with low support (remaining=771)
[2026-06-08T08:06:22] Filtering fusions with no coverage around the breakpoints (remaining=750)
[2026-06-08T08:06:23] Indexing gene sequences 
[2026-06-08T08:06:27] Filtering genes with >=30% identity (remaining=271)
[2026-06-08T08:06:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=104)
[2026-06-08T08:06:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=100)
[2026-06-08T08:06:30] Searching for additional isoforms (remaining=123)
[2026-06-08T08:06:31] Assigning confidence scores to events 
[2026-06-08T08:06:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:06:34] Writing fusions to file '659_ri-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:06:35] Writing discarded fusions to file '659_ri-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:06:55] Freeing resources
[2026-06-08T08:07:06] Done (elapsed time=00:08:41, CPU time=00:08:39, peak memory=11gb)