[2026-06-08T08:39:29] Launching Arriba 2.4.0
[2026-06-08T08:39:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:48] Reading chimeric alignments from '659_bGc-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11632255)
[2026-06-08T08:47:45] Marking multi-mapping alignments (marked=6965187)
[2026-06-08T08:47:50] Detecting strandedness (reverse)
[2026-06-08T08:47:50] Assigning strands to alignments 
[2026-06-08T08:47:52] Annotating alignments 
[2026-06-08T08:48:29] Filtering duplicates (remaining=4766084)
[2026-06-08T08:48:35] 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=4611416)
[2026-06-08T08:48:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4611416)
[2026-06-08T08:48:40] Filtering viral contigs with expression lower than the top 5 (remaining=4611416)
[2026-06-08T08:48:44] Filtering viral contigs with less than 5% coverage (remaining=4611416)
[2026-06-08T08:48:47] Estimating fragment length (mate gap mean=-90.4064, mate gap stddev=28.0126, read length mean=136.237)
[2026-06-08T08:48:47] Filtering read-through fragments with a distance <=10000bp (remaining=4364911)
[2026-06-08T08:48:49] Filtering inconsistently clipped mates (remaining=4304474)
[2026-06-08T08:48:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4137109)
[2026-06-08T08:48:55] Filtering fragments with small insert size (remaining=4136562)
[2026-06-08T08:48:57] Filtering alignments with long gaps (remaining=4136560)
[2026-06-08T08:48:59] Filtering fragments with both mates in the same gene (remaining=4135804)
[2026-06-08T08:49:01] Filtering fusions arising from hairpin structures (remaining=3953177)
[2026-06-08T08:49:03] Filtering reads with a mismatch p-value <=0.01 (remaining=1866482)
[2026-06-08T08:49:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=610529)
[2026-06-08T08:49:24] Finding fusions and counting supporting reads (total=510023)
[2026-06-08T08:49:39] Merging adjacent fusion breakpoints (remaining=506595)
[2026-06-08T08:49:40] Filtering multi-mapping fusions by alignment score and read support (remaining=314321)
[2026-06-08T08:50:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=312704)
[2026-06-08T08:50:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=166120)
[2026-06-08T08:50:21] Filtering fusions with <2 supporting reads (remaining=19488)
[2026-06-08T08:50:22] Filtering fusions with an e-value >=0.3 (remaining=5088)
[2026-06-08T08:50:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5138)
[2026-06-08T08:50:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5061)
[2026-06-08T08:50:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5062)
[2026-06-08T08:50:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4523)
[2026-06-08T08:50:32] Searching for fusions with spliced split reads (remaining=4612)
[2026-06-08T08:50:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=3248)
[2026-06-08T08:50:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3212)
[2026-06-08T08:50:38] Searching for fusions with >=4 spliced events (remaining=3594)
[2026-06-08T08:50:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1043)
[2026-06-08T08:50:55] Filtering fusions with anchors <=23nt (remaining=826)
[2026-06-08T08:50:56] Filtering end-to-end fusions with low support (remaining=798)
[2026-06-08T08:50:56] Filtering fusions with no coverage around the breakpoints (remaining=768)
[2026-06-08T08:50:57] Indexing gene sequences 
[2026-06-08T08:51:01] Filtering genes with >=30% identity (remaining=261)
[2026-06-08T08:51:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=141)
[2026-06-08T08:51:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=138)
[2026-06-08T08:51:06] Searching for additional isoforms (remaining=154)
[2026-06-08T08:51:07] Assigning confidence scores to events 
[2026-06-08T08:51:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:10] Writing fusions to file '659_bGc-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T08:51:11] Writing discarded fusions to file '659_bGc-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:34] Freeing resources
[2026-06-08T08:51:53] Done (elapsed time=00:12:24, CPU time=00:12:23, peak memory=15.9gb)