[2026-06-08T08:56:32] Launching Arriba 2.4.0
[2026-06-08T08:56:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:56:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:56:44] Reading chimeric alignments from '659_ezg-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=12460474)
[2026-06-08T09:04:08] Marking multi-mapping alignments (marked=7699544)
[2026-06-08T09:04:14] Detecting strandedness (reverse)
[2026-06-08T09:04:14] Assigning strands to alignments 
[2026-06-08T09:04:17] Annotating alignments 
[2026-06-08T09:04:59] Filtering duplicates (remaining=6864556)
[2026-06-08T09:05:07] 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=6646657)
[2026-06-08T09:05:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6646657)
[2026-06-08T09:05:12] Filtering viral contigs with expression lower than the top 5 (remaining=6646657)
[2026-06-08T09:05:18] Filtering viral contigs with less than 5% coverage (remaining=6646657)
[2026-06-08T09:05:21] Estimating fragment length (mate gap mean=-90.3471, mate gap stddev=28.4839, read length mean=137.195)
[2026-06-08T09:05:21] Filtering read-through fragments with a distance <=10000bp (remaining=6193862)
[2026-06-08T09:05:23] Filtering inconsistently clipped mates (remaining=6110100)
[2026-06-08T09:05:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5936305)
[2026-06-08T09:05:31] Filtering fragments with small insert size (remaining=5935623)
[2026-06-08T09:05:33] Filtering alignments with long gaps (remaining=5935623)
[2026-06-08T09:05:36] Filtering fragments with both mates in the same gene (remaining=5934744)
[2026-06-08T09:05:38] Filtering fusions arising from hairpin structures (remaining=5627449)
[2026-06-08T09:05:42] Filtering reads with a mismatch p-value <=0.01 (remaining=2883583)
[2026-06-08T09:05:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=1089981)
[2026-06-08T09:06:08] Finding fusions and counting supporting reads (total=842413)
[2026-06-08T09:06:27] Merging adjacent fusion breakpoints (remaining=833806)
[2026-06-08T09:06:29] Filtering multi-mapping fusions by alignment score and read support (remaining=518730)
[2026-06-08T09:07:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:07:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=516400)
[2026-06-08T09:07:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=268292)
[2026-06-08T09:07:18] Filtering fusions with <2 supporting reads (remaining=37547)
[2026-06-08T09:07:19] Filtering fusions with an e-value >=0.3 (remaining=10059)
[2026-06-08T09:07:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10108)
[2026-06-08T09:07:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9931)
[2026-06-08T09:07:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9934)
[2026-06-08T09:07:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7752)
[2026-06-08T09:07:32] Searching for fusions with spliced split reads (remaining=7768)
[2026-06-08T09:07:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=4828)
[2026-06-08T09:07:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4789)
[2026-06-08T09:07:40] Searching for fusions with >=4 spliced events (remaining=6035)
[2026-06-08T09:07:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2435)
[2026-06-08T09:07:56] Filtering fusions with anchors <=23nt (remaining=1985)
[2026-06-08T09:07:57] Filtering end-to-end fusions with low support (remaining=1940)
[2026-06-08T09:07:57] Filtering fusions with no coverage around the breakpoints (remaining=1904)
[2026-06-08T09:07:58] Indexing gene sequences 
[2026-06-08T09:08:04] Filtering genes with >=30% identity (remaining=581)
[2026-06-08T09:08:07] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=217)
[2026-06-08T09:08:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-08T09:08:11] Searching for additional isoforms (remaining=228)
[2026-06-08T09:08:13] Assigning confidence scores to events 
[2026-06-08T09:08:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:08:16] Writing fusions to file '659_ezg-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:08:18] Writing discarded fusions to file '659_ezg-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:49] Freeing resources
[2026-06-08T09:09:09] Done (elapsed time=00:12:37, CPU time=00:12:36, peak memory=17.1gb)