[2026-06-08T08:59:28] Launching Arriba 2.4.0
[2026-06-08T08:59:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:59:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:59:41] Reading chimeric alignments from '659_eHw-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=12951545)
[2026-06-08T09:07:56] Marking multi-mapping alignments (marked=8126380)
[2026-06-08T09:08:02] Detecting strandedness (reverse)
[2026-06-08T09:08:02] Assigning strands to alignments 
[2026-06-08T09:08:04] Annotating alignments 
[2026-06-08T09:08:46] Filtering duplicates (remaining=4974273)
[2026-06-08T09:08:53] 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=4691079)
[2026-06-08T09:08:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4691079)
[2026-06-08T09:08:59] Filtering viral contigs with expression lower than the top 5 (remaining=4691079)
[2026-06-08T09:09:05] Filtering viral contigs with less than 5% coverage (remaining=4691079)
[2026-06-08T09:09:08] Estimating fragment length (mate gap mean=-89.804, mate gap stddev=28.4515, read length mean=137.693)
[2026-06-08T09:09:08] Filtering read-through fragments with a distance <=10000bp (remaining=4456295)
[2026-06-08T09:09:10] Filtering inconsistently clipped mates (remaining=4390641)
[2026-06-08T09:09:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4242161)
[2026-06-08T09:09:18] Filtering fragments with small insert size (remaining=4241477)
[2026-06-08T09:09:20] Filtering alignments with long gaps (remaining=4241477)
[2026-06-08T09:09:23] Filtering fragments with both mates in the same gene (remaining=4240928)
[2026-06-08T09:09:26] Filtering fusions arising from hairpin structures (remaining=4039679)
[2026-06-08T09:09:29] Filtering reads with a mismatch p-value <=0.01 (remaining=1848893)
[2026-06-08T09:09:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=522021)
[2026-06-08T09:09:48] Finding fusions and counting supporting reads (total=414820)
[2026-06-08T09:10:06] Merging adjacent fusion breakpoints (remaining=411197)
[2026-06-08T09:10:07] Filtering multi-mapping fusions by alignment score and read support (remaining=261762)
[2026-06-08T09:10:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:10:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=259949)
[2026-06-08T09:10:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=135796)
[2026-06-08T09:10:53] Filtering fusions with <2 supporting reads (remaining=17510)
[2026-06-08T09:10:54] Filtering fusions with an e-value >=0.3 (remaining=5266)
[2026-06-08T09:10:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5297)
[2026-06-08T09:10:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5235)
[2026-06-08T09:10:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5235)
[2026-06-08T09:11:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3153)
[2026-06-08T09:11:05] Searching for fusions with spliced split reads (remaining=3203)
[2026-06-08T09:11:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=2276)
[2026-06-08T09:11:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2253)
[2026-06-08T09:11:12] Searching for fusions with >=4 spliced events (remaining=2525)
[2026-06-08T09:11:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=849)
[2026-06-08T09:11:26] Filtering fusions with anchors <=23nt (remaining=655)
[2026-06-08T09:11:26] Filtering end-to-end fusions with low support (remaining=641)
[2026-06-08T09:11:27] Filtering fusions with no coverage around the breakpoints (remaining=618)
[2026-06-08T09:11:27] Indexing gene sequences 
[2026-06-08T09:11:30] Filtering genes with >=30% identity (remaining=261)
[2026-06-08T09:11:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=136)
[2026-06-08T09:11:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=128)
[2026-06-08T09:11:35] Searching for additional isoforms (remaining=149)
[2026-06-08T09:11:36] Assigning confidence scores to events 
[2026-06-08T09:11:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:11:38] Writing fusions to file '659_eHw-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:11:39] Writing discarded fusions to file '659_eHw-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:12:01] Freeing resources
[2026-06-08T09:12:22] Done (elapsed time=00:12:54, CPU time=00:12:52, peak memory=17.1gb)