[2026-06-04T21:14:45] Launching Arriba 2.4.0
[2026-06-04T21:14:45] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:14:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:14:56] Reading chimeric alignments from '659_Mt-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11266777)
[2026-06-04T21:21:32] Marking multi-mapping alignments (marked=7314967)
[2026-06-04T21:21:37] Detecting strandedness (reverse)
[2026-06-04T21:21:37] Assigning strands to alignments 
[2026-06-04T21:21:39] Annotating alignments 
[2026-06-04T21:22:12] Filtering duplicates (remaining=5570600)
[2026-06-04T21:22:18] 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=5260930)
[2026-06-04T21:22:21] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5260930)
[2026-06-04T21:22:23] Filtering viral contigs with expression lower than the top 5 (remaining=5260930)
[2026-06-04T21:22:28] Filtering viral contigs with less than 5% coverage (remaining=5260930)
[2026-06-04T21:22:30] Estimating fragment length (mate gap mean=-86.0106, mate gap stddev=27.8061, read length mean=125.731)
[2026-06-04T21:22:31] Filtering read-through fragments with a distance <=10000bp (remaining=4973596)
[2026-06-04T21:22:33] Filtering inconsistently clipped mates (remaining=4857904)
[2026-06-04T21:22:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4699474)
[2026-06-04T21:22:39] Filtering fragments with small insert size (remaining=4698677)
[2026-06-04T21:22:42] Filtering alignments with long gaps (remaining=4698677)
[2026-06-04T21:22:44] Filtering fragments with both mates in the same gene (remaining=4697723)
[2026-06-04T21:22:46] Filtering fusions arising from hairpin structures (remaining=4378562)
[2026-06-04T21:22:49] Filtering reads with a mismatch p-value <=0.01 (remaining=2173479)
[2026-06-04T21:23:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=970067)
[2026-06-04T21:23:11] Finding fusions and counting supporting reads (total=619183)
[2026-06-04T21:23:26] Merging adjacent fusion breakpoints (remaining=609483)
[2026-06-04T21:23:28] Filtering multi-mapping fusions by alignment score and read support (remaining=365043)
[2026-06-04T21:24:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:24:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=363840)
[2026-06-04T21:24:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=213826)
[2026-06-04T21:24:08] Filtering fusions with <2 supporting reads (remaining=30416)
[2026-06-04T21:24:09] Filtering fusions with an e-value >=0.3 (remaining=6810)
[2026-06-04T21:24:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6878)
[2026-06-04T21:24:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6707)
[2026-06-04T21:24:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6707)
[2026-06-04T21:24:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6342)
[2026-06-04T21:24:20] Searching for fusions with spliced split reads (remaining=6482)
[2026-06-04T21:24:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=4300)
[2026-06-04T21:24:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4245)
[2026-06-04T21:24:26] Searching for fusions with >=4 spliced events (remaining=4944)
[2026-06-04T21:24:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1783)
[2026-06-04T21:24:40] Filtering fusions with anchors <=23nt (remaining=1441)
[2026-06-04T21:24:41] Filtering end-to-end fusions with low support (remaining=1397)
[2026-06-04T21:24:42] Filtering fusions with no coverage around the breakpoints (remaining=1357)
[2026-06-04T21:24:42] Indexing gene sequences 
[2026-06-04T21:24:48] Filtering genes with >=30% identity (remaining=408)
[2026-06-04T21:24:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=172)
[2026-06-04T21:24:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=167)
[2026-06-04T21:24:54] Searching for additional isoforms (remaining=201)
[2026-06-04T21:24:55] Assigning confidence scores to events 
[2026-06-04T21:24:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:24:58] Writing fusions to file '659_Mt-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:25:00] Writing discarded fusions to file '659_Mt-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:25:22] Freeing resources
[2026-06-04T21:25:40] Done (elapsed time=00:10:55, CPU time=00:10:54, peak memory=15.8gb)