[2026-06-08T08:27:06] Launching Arriba 2.4.0
[2026-06-08T08:27:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:15] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:19] Reading chimeric alignments from '659_buD-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=7998513)
[2026-06-08T08:32:21] Marking multi-mapping alignments (marked=4973709)
[2026-06-08T08:32:24] Detecting strandedness (reverse)
[2026-06-08T08:32:24] Assigning strands to alignments 
[2026-06-08T08:32:26] Annotating alignments 
[2026-06-08T08:32:58] Filtering duplicates (remaining=3826638)
[2026-06-08T08:33:03] 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=3687044)
[2026-06-08T08:33:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3687044)
[2026-06-08T08:33:07] Filtering viral contigs with expression lower than the top 5 (remaining=3687044)
[2026-06-08T08:33:11] Filtering viral contigs with less than 5% coverage (remaining=3687044)
[2026-06-08T08:33:13] Estimating fragment length (mate gap mean=-85.7674, mate gap stddev=28.4633, read length mean=129.927)
[2026-06-08T08:33:13] Filtering read-through fragments with a distance <=10000bp (remaining=3450288)
[2026-06-08T08:33:15] Filtering inconsistently clipped mates (remaining=3398626)
[2026-06-08T08:33:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3301841)
[2026-06-08T08:33:20] Filtering fragments with small insert size (remaining=3301328)
[2026-06-08T08:33:22] Filtering alignments with long gaps (remaining=3301327)
[2026-06-08T08:33:24] Filtering fragments with both mates in the same gene (remaining=3300622)
[2026-06-08T08:33:26] Filtering fusions arising from hairpin structures (remaining=3153102)
[2026-06-08T08:33:28] Filtering reads with a mismatch p-value <=0.01 (remaining=1357272)
[2026-06-08T08:33:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=580020)
[2026-06-08T08:33:44] Finding fusions and counting supporting reads (total=479789)
[2026-06-08T08:33:59] Merging adjacent fusion breakpoints (remaining=474916)
[2026-06-08T08:34:01] Filtering multi-mapping fusions by alignment score and read support (remaining=293416)
[2026-06-08T08:34:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=292036)
[2026-06-08T08:34:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=146666)
[2026-06-08T08:34:38] Filtering fusions with <2 supporting reads (remaining=19902)
[2026-06-08T08:34:39] Filtering fusions with an e-value >=0.3 (remaining=5733)
[2026-06-08T08:34:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5765)
[2026-06-08T08:34:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5703)
[2026-06-08T08:34:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5703)
[2026-06-08T08:34:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4672)
[2026-06-08T08:34:48] Searching for fusions with spliced split reads (remaining=4759)
[2026-06-08T08:34:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=3302)
[2026-06-08T08:34:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3253)
[2026-06-08T08:34:53] Searching for fusions with >=4 spliced events (remaining=3714)
[2026-06-08T08:34:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1328)
[2026-06-08T08:35:10] Filtering fusions with anchors <=23nt (remaining=1112)
[2026-06-08T08:35:11] Filtering end-to-end fusions with low support (remaining=1080)
[2026-06-08T08:35:11] Filtering fusions with no coverage around the breakpoints (remaining=1048)
[2026-06-08T08:35:12] Indexing gene sequences 
[2026-06-08T08:35:19] Filtering genes with >=30% identity (remaining=384)
[2026-06-08T08:35:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=198)
[2026-06-08T08:35:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=179)
[2026-06-08T08:35:24] Searching for additional isoforms (remaining=204)
[2026-06-08T08:35:25] Assigning confidence scores to events 
[2026-06-08T08:35:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:28] Writing fusions to file '659_buD-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:35:30] Writing discarded fusions to file '659_buD-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:57] Freeing resources
[2026-06-08T08:36:15] Done (elapsed time=00:09:09, CPU time=00:09:07, peak memory=12.4gb)