[2026-06-08T09:11:32] Launching Arriba 2.4.0
[2026-06-08T09:11:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:11:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:11:45] Reading chimeric alignments from '659_bua-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11491464)
[2026-06-08T09:18:53] Marking multi-mapping alignments (marked=6989056)
[2026-06-08T09:18:57] Detecting strandedness (reverse)
[2026-06-08T09:18:57] Assigning strands to alignments 
[2026-06-08T09:19:00] Annotating alignments 
[2026-06-08T09:19:38] Filtering duplicates (remaining=5642693)
[2026-06-08T09:19:45] 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=5488568)
[2026-06-08T09:19:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5488568)
[2026-06-08T09:19:49] Filtering viral contigs with expression lower than the top 5 (remaining=5488568)
[2026-06-08T09:19:54] Filtering viral contigs with less than 5% coverage (remaining=5488568)
[2026-06-08T09:19:57] Estimating fragment length (mate gap mean=-89.5843, mate gap stddev=28.5418, read length mean=137.594)
[2026-06-08T09:19:57] Filtering read-through fragments with a distance <=10000bp (remaining=5219064)
[2026-06-08T09:20:00] Filtering inconsistently clipped mates (remaining=5145195)
[2026-06-08T09:20:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4959940)
[2026-06-08T09:20:07] Filtering fragments with small insert size (remaining=4959295)
[2026-06-08T09:20:09] Filtering alignments with long gaps (remaining=4959295)
[2026-06-08T09:20:11] Filtering fragments with both mates in the same gene (remaining=4958491)
[2026-06-08T09:20:14] Filtering fusions arising from hairpin structures (remaining=4726664)
[2026-06-08T09:20:16] Filtering reads with a mismatch p-value <=0.01 (remaining=2243000)
[2026-06-08T09:20:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=692559)
[2026-06-08T09:20:38] Finding fusions and counting supporting reads (total=547414)
[2026-06-08T09:20:54] Merging adjacent fusion breakpoints (remaining=543604)
[2026-06-08T09:20:55] Filtering multi-mapping fusions by alignment score and read support (remaining=350717)
[2026-06-08T09:21:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:21:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=348593)
[2026-06-08T09:21:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=190359)
[2026-06-08T09:21:39] Filtering fusions with <2 supporting reads (remaining=25682)
[2026-06-08T09:21:40] Filtering fusions with an e-value >=0.3 (remaining=7883)
[2026-06-08T09:21:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7919)
[2026-06-08T09:21:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7846)
[2026-06-08T09:21:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7848)
[2026-06-08T09:21:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5236)
[2026-06-08T09:21:52] Searching for fusions with spliced split reads (remaining=5344)
[2026-06-08T09:21:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=3466)
[2026-06-08T09:21:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3434)
[2026-06-08T09:21:59] Searching for fusions with >=4 spliced events (remaining=4159)
[2026-06-08T09:22:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1482)
[2026-06-08T09:22:13] Filtering fusions with anchors <=23nt (remaining=1248)
[2026-06-08T09:22:14] Filtering end-to-end fusions with low support (remaining=1217)
[2026-06-08T09:22:14] Filtering fusions with no coverage around the breakpoints (remaining=1179)
[2026-06-08T09:22:15] Indexing gene sequences 
[2026-06-08T09:22:20] Filtering genes with >=30% identity (remaining=339)
[2026-06-08T09:22:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=140)
[2026-06-08T09:22:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=124)
[2026-06-08T09:22:25] Searching for additional isoforms (remaining=170)
[2026-06-08T09:22:27] Assigning confidence scores to events 
[2026-06-08T09:22:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:22:30] Writing fusions to file '659_bua-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:22:31] Writing discarded fusions to file '659_bua-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:22:56] Freeing resources
[2026-06-08T09:23:20] Done (elapsed time=00:11:48, CPU time=00:11:46, peak memory=15.7gb)