[2026-06-08T08:54:36] Launching Arriba 2.4.0
[2026-06-08T08:54:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:51] Reading chimeric alignments from '659_cWx-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=13911027)
[2026-06-08T09:01:56] Marking multi-mapping alignments (marked=8864023)
[2026-06-08T09:02:02] Detecting strandedness (reverse)
[2026-06-08T09:02:02] Assigning strands to alignments 
[2026-06-08T09:02:04] Annotating alignments 
[2026-06-08T09:02:42] Filtering duplicates (remaining=7192496)
[2026-06-08T09:02:50] 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=6932534)
[2026-06-08T09:02:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6932534)
[2026-06-08T09:02:55] Filtering viral contigs with expression lower than the top 5 (remaining=6932534)
[2026-06-08T09:03:00] Filtering viral contigs with less than 5% coverage (remaining=6932534)
[2026-06-08T09:03:03] Estimating fragment length (mate gap mean=-87.5521, mate gap stddev=29.5642, read length mean=137.163)
[2026-06-08T09:03:03] Filtering read-through fragments with a distance <=10000bp (remaining=6548856)
[2026-06-08T09:03:05] Filtering inconsistently clipped mates (remaining=6460554)
[2026-06-08T09:03:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6238900)
[2026-06-08T09:03:12] Filtering fragments with small insert size (remaining=6238240)
[2026-06-08T09:03:14] Filtering alignments with long gaps (remaining=6238240)
[2026-06-08T09:03:17] Filtering fragments with both mates in the same gene (remaining=6237363)
[2026-06-08T09:03:19] Filtering fusions arising from hairpin structures (remaining=5945939)
[2026-06-08T09:03:22] Filtering reads with a mismatch p-value <=0.01 (remaining=2854578)
[2026-06-08T09:03:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=835726)
[2026-06-08T09:03:47] Finding fusions and counting supporting reads (total=685668)
[2026-06-08T09:04:05] Merging adjacent fusion breakpoints (remaining=679302)
[2026-06-08T09:04:07] Filtering multi-mapping fusions by alignment score and read support (remaining=410535)
[2026-06-08T09:04:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=406687)
[2026-06-08T09:04:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=224873)
[2026-06-08T09:04:52] Filtering fusions with <2 supporting reads (remaining=28821)
[2026-06-08T09:04:53] Filtering fusions with an e-value >=0.3 (remaining=9399)
[2026-06-08T09:04:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9457)
[2026-06-08T09:04:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9333)
[2026-06-08T09:04:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9336)
[2026-06-08T09:05:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6488)
[2026-06-08T09:05:06] Searching for fusions with spliced split reads (remaining=6598)
[2026-06-08T09:05:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=4047)
[2026-06-08T09:05:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4003)
[2026-06-08T09:05:14] Searching for fusions with >=4 spliced events (remaining=4734)
[2026-06-08T09:05:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1755)
[2026-06-08T09:05:31] Filtering fusions with anchors <=23nt (remaining=1370)
[2026-06-08T09:05:32] Filtering end-to-end fusions with low support (remaining=1316)
[2026-06-08T09:05:32] Filtering fusions with no coverage around the breakpoints (remaining=1270)
[2026-06-08T09:05:33] Indexing gene sequences 
[2026-06-08T09:05:39] Filtering genes with >=30% identity (remaining=400)
[2026-06-08T09:05:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=147)
[2026-06-08T09:05:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=136)
[2026-06-08T09:05:44] Searching for additional isoforms (remaining=182)
[2026-06-08T09:05:46] Assigning confidence scores to events 
[2026-06-08T09:05:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:49] Writing fusions to file '659_cWx-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:50] Writing discarded fusions to file '659_cWx-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:17] Freeing resources
[2026-06-08T09:06:38] Done (elapsed time=00:12:02, CPU time=00:12:01, peak memory=18.2gb)