[2026-06-08T08:57:31] Launching Arriba 2.4.0
[2026-06-08T08:57:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:57:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:57:43] Reading chimeric alignments from '659_bNS-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=12354883)
[2026-06-08T09:05:57] Marking multi-mapping alignments (marked=7495165)
[2026-06-08T09:06:03] Detecting strandedness (reverse)
[2026-06-08T09:06:03] Assigning strands to alignments 
[2026-06-08T09:06:06] Annotating alignments 
[2026-06-08T09:06:57] Filtering duplicates (remaining=7110387)
[2026-06-08T09:07:07] 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=6933769)
[2026-06-08T09:07:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6933769)
[2026-06-08T09:07:13] Filtering viral contigs with expression lower than the top 5 (remaining=6933769)
[2026-06-08T09:07:20] Filtering viral contigs with less than 5% coverage (remaining=6933769)
[2026-06-08T09:07:23] Estimating fragment length (mate gap mean=-89.9895, mate gap stddev=29.087, read length mean=138.479)
[2026-06-08T09:07:23] Filtering read-through fragments with a distance <=10000bp (remaining=6537612)
[2026-06-08T09:07:26] Filtering inconsistently clipped mates (remaining=6458615)
[2026-06-08T09:07:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6258550)
[2026-06-08T09:07:35] Filtering fragments with small insert size (remaining=6257897)
[2026-06-08T09:07:38] Filtering alignments with long gaps (remaining=6257897)
[2026-06-08T09:07:41] Filtering fragments with both mates in the same gene (remaining=6257016)
[2026-06-08T09:07:45] Filtering fusions arising from hairpin structures (remaining=5920161)
[2026-06-08T09:07:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2913321)
[2026-06-08T09:08:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=1080478)
[2026-06-08T09:08:20] Finding fusions and counting supporting reads (total=835757)
[2026-06-08T09:08:46] Merging adjacent fusion breakpoints (remaining=828228)
[2026-06-08T09:08:49] Filtering multi-mapping fusions by alignment score and read support (remaining=541986)
[2026-06-08T09:09:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:09:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=539653)
[2026-06-08T09:09:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=282953)
[2026-06-08T09:09:51] Filtering fusions with <2 supporting reads (remaining=37542)
[2026-06-08T09:09:52] Filtering fusions with an e-value >=0.3 (remaining=11194)
[2026-06-08T09:09:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11244)
[2026-06-08T09:09:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11153)
[2026-06-08T09:09:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11153)
[2026-06-08T09:10:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7542)
[2026-06-08T09:10:08] Searching for fusions with spliced split reads (remaining=7654)
[2026-06-08T09:10:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=4547)
[2026-06-08T09:10:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4488)
[2026-06-08T09:10:18] Searching for fusions with >=4 spliced events (remaining=5452)
[2026-06-08T09:10:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1859)
[2026-06-08T09:10:34] Filtering fusions with anchors <=23nt (remaining=1482)
[2026-06-08T09:10:35] Filtering end-to-end fusions with low support (remaining=1436)
[2026-06-08T09:10:36] Filtering fusions with no coverage around the breakpoints (remaining=1404)
[2026-06-08T09:10:36] Indexing gene sequences 
[2026-06-08T09:10:43] Filtering genes with >=30% identity (remaining=411)
[2026-06-08T09:10:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=179)
[2026-06-08T09:10:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=171)
[2026-06-08T09:10:54] Searching for additional isoforms (remaining=214)
[2026-06-08T09:10:55] Assigning confidence scores to events 
[2026-06-08T09:10:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:10:59] Writing fusions to file '659_bNS-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:11:01] Writing discarded fusions to file '659_bNS-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:11:38] Freeing resources
[2026-06-08T09:12:03] Done (elapsed time=00:14:32, CPU time=00:14:31, peak memory=16.9gb)