[2026-06-08T08:25:04] Launching Arriba 2.4.0
[2026-06-08T08:25:04] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:21] Reading chimeric alignments from '659_dts-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=7916996)
[2026-06-08T08:30:24] Marking multi-mapping alignments (marked=5009833)
[2026-06-08T08:30:27] Detecting strandedness (reverse)
[2026-06-08T08:30:27] Assigning strands to alignments 
[2026-06-08T08:30:29] Annotating alignments 
[2026-06-08T08:30:54] Filtering duplicates (remaining=3012728)
[2026-06-08T08:30:58] 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=2902687)
[2026-06-08T08:30:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2902687)
[2026-06-08T08:31:01] Filtering viral contigs with expression lower than the top 5 (remaining=2902687)
[2026-06-08T08:31:04] Filtering viral contigs with less than 5% coverage (remaining=2902687)
[2026-06-08T08:31:05] Estimating fragment length (mate gap mean=-86.485, mate gap stddev=27.9214, read length mean=128.197)
[2026-06-08T08:31:05] Filtering read-through fragments with a distance <=10000bp (remaining=2711924)
[2026-06-08T08:31:07] Filtering inconsistently clipped mates (remaining=2668236)
[2026-06-08T08:31:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2584735)
[2026-06-08T08:31:11] Filtering fragments with small insert size (remaining=2584324)
[2026-06-08T08:31:12] Filtering alignments with long gaps (remaining=2584324)
[2026-06-08T08:31:14] Filtering fragments with both mates in the same gene (remaining=2583741)
[2026-06-08T08:31:15] Filtering fusions arising from hairpin structures (remaining=2480957)
[2026-06-08T08:31:17] Filtering reads with a mismatch p-value <=0.01 (remaining=1007690)
[2026-06-08T08:31:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=402046)
[2026-06-08T08:31:29] Finding fusions and counting supporting reads (total=363238)
[2026-06-08T08:31:41] Merging adjacent fusion breakpoints (remaining=359368)
[2026-06-08T08:31:41] Filtering multi-mapping fusions by alignment score and read support (remaining=212848)
[2026-06-08T08:32:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:13] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=211261)
[2026-06-08T08:32:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=107400)
[2026-06-08T08:32:14] Filtering fusions with <2 supporting reads (remaining=11805)
[2026-06-08T08:32:14] Filtering fusions with an e-value >=0.3 (remaining=3485)
[2026-06-08T08:32:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3512)
[2026-06-08T08:32:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3448)
[2026-06-08T08:32:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3448)
[2026-06-08T08:32:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3122)
[2026-06-08T08:32:21] Searching for fusions with spliced split reads (remaining=3167)
[2026-06-08T08:32:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=2290)
[2026-06-08T08:32:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2263)
[2026-06-08T08:32:27] Searching for fusions with >=4 spliced events (remaining=2444)
[2026-06-08T08:32:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=777)
[2026-06-08T08:32:43] Filtering fusions with anchors <=23nt (remaining=586)
[2026-06-08T08:32:44] Filtering end-to-end fusions with low support (remaining=574)
[2026-06-08T08:32:44] Filtering fusions with no coverage around the breakpoints (remaining=554)
[2026-06-08T08:32:44] Indexing gene sequences 
[2026-06-08T08:32:47] Filtering genes with >=30% identity (remaining=210)
[2026-06-08T08:32:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=112)
[2026-06-08T08:32:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=107)
[2026-06-08T08:32:51] Searching for additional isoforms (remaining=122)
[2026-06-08T08:32:52] Assigning confidence scores to events 
[2026-06-08T08:32:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:53] Writing fusions to file '659_dts-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:32:54] Writing discarded fusions to file '659_dts-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:33:10] Freeing resources
[2026-06-08T08:33:22] Done (elapsed time=00:08:18, CPU time=00:08:18, peak memory=12.2gb)