[2026-06-08T08:26:47] Launching Arriba 2.4.0
[2026-06-08T08:26:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:03] Reading chimeric alignments from '659_Mt-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11266777)
[2026-06-08T08:33:40] Marking multi-mapping alignments (marked=7314967)
[2026-06-08T08:33:45] Detecting strandedness (reverse)
[2026-06-08T08:33:45] Assigning strands to alignments 
[2026-06-08T08:33:47] Annotating alignments 
[2026-06-08T08:34:18] Filtering duplicates (remaining=5570600)
[2026-06-08T08:34:24] 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)
[2026-06-08T08:34:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5260930)
[2026-06-08T08:34:28] Filtering viral contigs with expression lower than the top 5 (remaining=5260930)
[2026-06-08T08:34:33] Filtering viral contigs with less than 5% coverage (remaining=5260930)
[2026-06-08T08:34:35] Estimating fragment length (mate gap mean=-86.0106, mate gap stddev=27.8061, read length mean=125.731)
[2026-06-08T08:34:35] Filtering read-through fragments with a distance <=10000bp (remaining=4973596)
[2026-06-08T08:34:37] Filtering inconsistently clipped mates (remaining=4857904)
[2026-06-08T08:34:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4699474)
[2026-06-08T08:34:43] Filtering fragments with small insert size (remaining=4698677)
[2026-06-08T08:34:45] Filtering alignments with long gaps (remaining=4698677)
[2026-06-08T08:34:47] Filtering fragments with both mates in the same gene (remaining=4697723)
[2026-06-08T08:34:49] Filtering fusions arising from hairpin structures (remaining=4378562)
[2026-06-08T08:34:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2173479)
[2026-06-08T08:35:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=970067)
[2026-06-08T08:35:14] Finding fusions and counting supporting reads (total=619183)
[2026-06-08T08:35:28] Merging adjacent fusion breakpoints (remaining=609483)
[2026-06-08T08:35:29] Filtering multi-mapping fusions by alignment score and read support (remaining=365043)
[2026-06-08T08:35:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=363840)
[2026-06-08T08:36:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=213826)
[2026-06-08T08:36:05] Filtering fusions with <2 supporting reads (remaining=30416)
[2026-06-08T08:36:06] Filtering fusions with an e-value >=0.3 (remaining=6810)
[2026-06-08T08:36:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6878)
[2026-06-08T08:36:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6707)
[2026-06-08T08:36:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6707)
[2026-06-08T08:36:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6342)
[2026-06-08T08:36:16] Searching for fusions with spliced split reads (remaining=6482)
[2026-06-08T08:36:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4300)
[2026-06-08T08:36:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4245)
[2026-06-08T08:36:22] Searching for fusions with >=4 spliced events (remaining=4944)
[2026-06-08T08:36:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1783)
[2026-06-08T08:36:36] Filtering fusions with anchors <=23nt (remaining=1441)
[2026-06-08T08:36:37] Filtering end-to-end fusions with low support (remaining=1397)
[2026-06-08T08:36:37] Filtering fusions with no coverage around the breakpoints (remaining=1357)
[2026-06-08T08:36:38] Indexing gene sequences 
[2026-06-08T08:36:43] Filtering genes with >=30% identity (remaining=408)
[2026-06-08T08:36:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=172)
[2026-06-08T08:36:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=167)
[2026-06-08T08:36:49] Searching for additional isoforms (remaining=201)
[2026-06-08T08:36:50] Assigning confidence scores to events 
[2026-06-08T08:36:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:53] Writing fusions to file '659_Mt-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:54] Writing discarded fusions to file '659_Mt-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:16] Freeing resources
[2026-06-08T08:37:32] Done (elapsed time=00:10:45, CPU time=00:10:44, peak memory=15.8gb)