[2026-06-08T08:39:52] Launching Arriba 2.4.0
[2026-06-08T08:39:52] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:04] Reading chimeric alignments from '659_bQZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11117234)
[2026-06-08T08:47:20] Marking multi-mapping alignments (marked=6974716)
[2026-06-08T08:47:25] Detecting strandedness (no)
[2026-06-08T08:47:25] Annotating alignments 
[2026-06-08T08:48:12] Filtering duplicates (remaining=6218336)
[2026-06-08T08:48:22] 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=5917988)
[2026-06-08T08:48:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5917988)
[2026-06-08T08:48:27] Filtering viral contigs with expression lower than the top 5 (remaining=5917988)
[2026-06-08T08:48:33] Filtering viral contigs with less than 5% coverage (remaining=5917988)
[2026-06-08T08:48:36] Estimating fragment length (mate gap mean=-89.0883, mate gap stddev=28.1685, read length mean=133.083)
[2026-06-08T08:48:36] Filtering read-through fragments with a distance <=10000bp (remaining=5499756)
[2026-06-08T08:48:38] Filtering inconsistently clipped mates (remaining=5390719)
[2026-06-08T08:48:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5185028)
[2026-06-08T08:48:45] Filtering fragments with small insert size (remaining=5184079)
[2026-06-08T08:48:47] Filtering alignments with long gaps (remaining=5184079)
[2026-06-08T08:48:49] Filtering fragments with both mates in the same gene (remaining=5183100)
[2026-06-08T08:48:52] Filtering fusions arising from hairpin structures (remaining=4812876)
[2026-06-08T08:48:54] Filtering reads with a mismatch p-value <=0.01 (remaining=2490804)
[2026-06-08T08:49:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=1113814)
[2026-06-08T08:49:19] Finding fusions and counting supporting reads (total=823171)
[2026-06-08T08:49:33] Merging adjacent fusion breakpoints (remaining=811266)
[2026-06-08T08:49:35] Filtering multi-mapping fusions by alignment score and read support (remaining=509710)
[2026-06-08T08:50:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=507672)
[2026-06-08T08:50:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=262880)
[2026-06-08T08:50:16] Filtering fusions with <2 supporting reads (remaining=37496)
[2026-06-08T08:50:17] Filtering fusions with an e-value >=0.3 (remaining=10155)
[2026-06-08T08:50:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10212)
[2026-06-08T08:50:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10104)
[2026-06-08T08:50:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10106)
[2026-06-08T08:50:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7494)
[2026-06-08T08:50:28] Searching for fusions with spliced split reads (remaining=7595)
[2026-06-08T08:50:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=4837)
[2026-06-08T08:50:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4797)
[2026-06-08T08:50:35] Searching for fusions with >=4 spliced events (remaining=5636)
[2026-06-08T08:50:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1987)
[2026-06-08T08:50:51] Filtering fusions with anchors <=23nt (remaining=1544)
[2026-06-08T08:50:52] Filtering end-to-end fusions with low support (remaining=1490)
[2026-06-08T08:50:53] Filtering fusions with no coverage around the breakpoints (remaining=1445)
[2026-06-08T08:50:53] Indexing gene sequences 
[2026-06-08T08:50:59] Filtering genes with >=30% identity (remaining=450)
[2026-06-08T08:51:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=180)
[2026-06-08T08:51:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=178)
[2026-06-08T08:51:05] Searching for additional isoforms (remaining=226)
[2026-06-08T08:51:06] Assigning confidence scores to events 
[2026-06-08T08:51:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:09] Writing fusions to file '659_bQZ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:11] Writing discarded fusions to file '659_bQZ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:41] Freeing resources
[2026-06-08T08:51:59] Done (elapsed time=00:12:07, CPU time=00:12:06, peak memory=15.9gb)