[2026-06-08T08:41:33] Launching Arriba 2.4.0
[2026-06-08T08:41:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:48] Reading chimeric alignments from '659_bua-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=11050472)
[2026-06-08T08:48:29] Marking multi-mapping alignments (marked=6607924)
[2026-06-08T08:48:32] Detecting strandedness (reverse)
[2026-06-08T08:48:32] Assigning strands to alignments 
[2026-06-08T08:48:34] Annotating alignments 
[2026-06-08T08:49:03] Filtering duplicates (remaining=6831690)
[2026-06-08T08:49:09] 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=6659690)
[2026-06-08T08:49:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6659690)
[2026-06-08T08:49:13] Filtering viral contigs with expression lower than the top 5 (remaining=6659690)
[2026-06-08T08:49:17] Filtering viral contigs with less than 5% coverage (remaining=6659690)
[2026-06-08T08:49:19] Estimating fragment length (mate gap mean=-89.6114, mate gap stddev=28.0187, read length mean=136.019)
[2026-06-08T08:49:19] Filtering read-through fragments with a distance <=10000bp (remaining=6264171)
[2026-06-08T08:49:21] Filtering inconsistently clipped mates (remaining=6157069)
[2026-06-08T08:49:23] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5970915)
[2026-06-08T08:49:26] Filtering fragments with small insert size (remaining=5970159)
[2026-06-08T08:49:28] Filtering alignments with long gaps (remaining=5970159)
[2026-06-08T08:49:30] Filtering fragments with both mates in the same gene (remaining=5969109)
[2026-06-08T08:49:32] Filtering fusions arising from hairpin structures (remaining=5582098)
[2026-06-08T08:49:34] Filtering reads with a mismatch p-value <=0.01 (remaining=2874400)
[2026-06-08T08:49:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=1043718)
[2026-06-08T08:49:57] Finding fusions and counting supporting reads (total=791104)
[2026-06-08T08:50:12] Merging adjacent fusion breakpoints (remaining=783683)
[2026-06-08T08:50:13] Filtering multi-mapping fusions by alignment score and read support (remaining=517720)
[2026-06-08T08:50:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=515419)
[2026-06-08T08:50:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=282115)
[2026-06-08T08:50:50] Filtering fusions with <2 supporting reads (remaining=38779)
[2026-06-08T08:50:50] Filtering fusions with an e-value >=0.3 (remaining=11055)
[2026-06-08T08:50:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11109)
[2026-06-08T08:50:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10971)
[2026-06-08T08:50:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10980)
[2026-06-08T08:50:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7351)
[2026-06-08T08:51:01] Searching for fusions with spliced split reads (remaining=7370)
[2026-06-08T08:51:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=4500)
[2026-06-08T08:51:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4446)
[2026-06-08T08:51:08] Searching for fusions with >=4 spliced events (remaining=5650)
[2026-06-08T08:51:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2205)
[2026-06-08T08:51:22] Filtering fusions with anchors <=23nt (remaining=1867)
[2026-06-08T08:51:23] Filtering end-to-end fusions with low support (remaining=1822)
[2026-06-08T08:51:24] Filtering fusions with no coverage around the breakpoints (remaining=1770)
[2026-06-08T08:51:25] Indexing gene sequences 
[2026-06-08T08:51:30] Filtering genes with >=30% identity (remaining=468)
[2026-06-08T08:51:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=168)
[2026-06-08T08:51:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=152)
[2026-06-08T08:51:37] Searching for additional isoforms (remaining=244)
[2026-06-08T08:51:39] Assigning confidence scores to events 
[2026-06-08T08:51:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:41] Writing fusions to file '659_bua-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:44] Writing discarded fusions to file '659_bua-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:09] Freeing resources
[2026-06-08T08:52:29] Done (elapsed time=00:10:56, CPU time=00:10:54, peak memory=15.6gb)