[2026-06-08T08:37:48] Launching Arriba 2.4.0
[2026-06-08T08:37:48] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:03] Reading chimeric alignments from '659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12790447)
[2026-06-08T08:45:04] Marking multi-mapping alignments (marked=8285198)
[2026-06-08T08:45:09] Detecting strandedness (reverse)
[2026-06-08T08:45:09] Assigning strands to alignments 
[2026-06-08T08:45:11] Annotating alignments 
[2026-06-08T08:45:47] Filtering duplicates (remaining=5421054)
[2026-06-08T08:45:52] 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=4744055)
[2026-06-08T08:45:55] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4744055)
[2026-06-08T08:45:57] Filtering viral contigs with expression lower than the top 5 (remaining=4744055)
[2026-06-08T08:46:02] Filtering viral contigs with less than 5% coverage (remaining=4744055)
[2026-06-08T08:46:04] Estimating fragment length (mate gap mean=-86.5772, mate gap stddev=27.96, read length mean=126.619)
[2026-06-08T08:46:04] Filtering read-through fragments with a distance <=10000bp (remaining=4480345)
[2026-06-08T08:46:06] Filtering inconsistently clipped mates (remaining=4375664)
[2026-06-08T08:46:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4229412)
[2026-06-08T08:46:12] Filtering fragments with small insert size (remaining=4227857)
[2026-06-08T08:46:14] Filtering alignments with long gaps (remaining=4227857)
[2026-06-08T08:46:16] Filtering fragments with both mates in the same gene (remaining=4226941)
[2026-06-08T08:46:18] Filtering fusions arising from hairpin structures (remaining=3934462)
[2026-06-08T08:46:21] Filtering reads with a mismatch p-value <=0.01 (remaining=1801281)
[2026-06-08T08:46:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=746689)
[2026-06-08T08:46:42] Finding fusions and counting supporting reads (total=610114)
[2026-06-08T08:46:57] Merging adjacent fusion breakpoints (remaining=599484)
[2026-06-08T08:46:58] Filtering multi-mapping fusions by alignment score and read support (remaining=330546)
[2026-06-08T08:47:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=327459)
[2026-06-08T08:47:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=176384)
[2026-06-08T08:47:33] Filtering fusions with <2 supporting reads (remaining=19507)
[2026-06-08T08:47:34] Filtering fusions with an e-value >=0.3 (remaining=5078)
[2026-06-08T08:47:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5134)
[2026-06-08T08:47:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4939)
[2026-06-08T08:47:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4941)
[2026-06-08T08:47:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4038)
[2026-06-08T08:47:44] Searching for fusions with spliced split reads (remaining=4094)
[2026-06-08T08:47:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=2840)
[2026-06-08T08:47:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2815)
[2026-06-08T08:47:50] Searching for fusions with >=4 spliced events (remaining=3072)
[2026-06-08T08:47:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1248)
[2026-06-08T08:48:09] Filtering fusions with anchors <=23nt (remaining=803)
[2026-06-08T08:48:09] Filtering end-to-end fusions with low support (remaining=777)
[2026-06-08T08:48:10] Filtering fusions with no coverage around the breakpoints (remaining=758)
[2026-06-08T08:48:10] Indexing gene sequences 
[2026-06-08T08:48:13] Filtering genes with >=30% identity (remaining=301)
[2026-06-08T08:48:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=147)
[2026-06-08T08:48:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-06-08T08:48:17] Searching for additional isoforms (remaining=157)
[2026-06-08T08:48:18] Assigning confidence scores to events 
[2026-06-08T08:48:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:21] Writing fusions to file '659_epZ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:22] Writing discarded fusions to file '659_epZ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:42] Freeing resources
[2026-06-08T08:49:00] Done (elapsed time=00:11:12, CPU time=00:11:11, peak memory=17.5gb)