[2026-06-08T08:51:28] Launching Arriba 2.4.0
[2026-06-08T08:51:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:41] Reading chimeric alignments from '659_bQZ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=11197114)
[2026-06-08T08:58:16] Marking multi-mapping alignments (marked=6920007)
[2026-06-08T08:58:22] Detecting strandedness (reverse)
[2026-06-08T08:58:22] Assigning strands to alignments 
[2026-06-08T08:58:24] Annotating alignments 
[2026-06-08T08:59:05] Filtering duplicates (remaining=5929076)
[2026-06-08T08:59:13] 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=5753380)
[2026-06-08T08:59:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5753380)
[2026-06-08T08:59:18] Filtering viral contigs with expression lower than the top 5 (remaining=5753380)
[2026-06-08T08:59:24] Filtering viral contigs with less than 5% coverage (remaining=5753380)
[2026-06-08T08:59:26] Estimating fragment length (mate gap mean=-90.7365, mate gap stddev=28.7726, read length mean=138.222)
[2026-06-08T08:59:27] Filtering read-through fragments with a distance <=10000bp (remaining=5391354)
[2026-06-08T08:59:29] Filtering inconsistently clipped mates (remaining=5319199)
[2026-06-08T08:59:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5114000)
[2026-06-08T08:59:37] Filtering fragments with small insert size (remaining=5113469)
[2026-06-08T08:59:39] Filtering alignments with long gaps (remaining=5113469)
[2026-06-08T08:59:42] Filtering fragments with both mates in the same gene (remaining=5112665)
[2026-06-08T08:59:45] Filtering fusions arising from hairpin structures (remaining=4842465)
[2026-06-08T08:59:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2460831)
[2026-06-08T09:00:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=873425)
[2026-06-08T09:00:12] Finding fusions and counting supporting reads (total=693108)
[2026-06-08T09:00:31] Merging adjacent fusion breakpoints (remaining=686366)
[2026-06-08T09:00:33] Filtering multi-mapping fusions by alignment score and read support (remaining=430355)
[2026-06-08T09:01:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=428279)
[2026-06-08T09:01:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=230373)
[2026-06-08T09:01:21] Filtering fusions with <2 supporting reads (remaining=32561)
[2026-06-08T09:01:22] Filtering fusions with an e-value >=0.3 (remaining=10073)
[2026-06-08T09:01:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10124)
[2026-06-08T09:01:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10048)
[2026-06-08T09:01:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10050)
[2026-06-08T09:01:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6688)
[2026-06-08T09:01:34] Searching for fusions with spliced split reads (remaining=6823)
[2026-06-08T09:01:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=4323)
[2026-06-08T09:01:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4294)
[2026-06-08T09:01:42] Searching for fusions with >=4 spliced events (remaining=5011)
[2026-06-08T09:01:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1736)
[2026-06-08T09:01:58] Filtering fusions with anchors <=23nt (remaining=1421)
[2026-06-08T09:01:58] Filtering end-to-end fusions with low support (remaining=1365)
[2026-06-08T09:01:59] Filtering fusions with no coverage around the breakpoints (remaining=1321)
[2026-06-08T09:02:00] Indexing gene sequences 
[2026-06-08T09:02:05] Filtering genes with >=30% identity (remaining=420)
[2026-06-08T09:02:07] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=170)
[2026-06-08T09:02:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=165)
[2026-06-08T09:02:11] Searching for additional isoforms (remaining=193)
[2026-06-08T09:02:12] Assigning confidence scores to events 
[2026-06-08T09:02:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:15] Writing fusions to file '659_bQZ-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:02:17] Writing discarded fusions to file '659_bQZ-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:02:48] Freeing resources
[2026-06-08T09:03:08] Done (elapsed time=00:11:40, CPU time=00:11:38, peak memory=15.7gb)