[2026-06-08T07:45:46] Launching Arriba 2.4.0
[2026-06-08T07:45:46] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:46:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:46:09] Reading chimeric alignments from '659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3144839)
[2026-06-08T07:48:31] Marking multi-mapping alignments (marked=2163582)
[2026-06-08T07:48:32] Detecting strandedness (reverse)
[2026-06-08T07:48:32] Assigning strands to alignments 
[2026-06-08T07:48:33] Annotating alignments 
[2026-06-08T07:48:44] Filtering duplicates (remaining=787763)
[2026-06-08T07:48:45] 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=702532)
[2026-06-08T07:48:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=702532)
[2026-06-08T07:48:47] Filtering viral contigs with expression lower than the top 5 (remaining=702532)
[2026-06-08T07:48:48] Filtering viral contigs with less than 5% coverage (remaining=702532)
[2026-06-08T07:48:49] Estimating fragment length (mate gap mean=-79.044, mate gap stddev=28.4224, read length mean=120.458)
[2026-06-08T07:48:49] Filtering read-through fragments with a distance <=10000bp (remaining=684007)
[2026-06-08T07:48:50] Filtering inconsistently clipped mates (remaining=667263)
[2026-06-08T07:48:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=622988)
[2026-06-08T07:48:51] Filtering fragments with small insert size (remaining=622690)
[2026-06-08T07:48:52] Filtering alignments with long gaps (remaining=622690)
[2026-06-08T07:48:52] Filtering fragments with both mates in the same gene (remaining=622380)
[2026-06-08T07:48:53] Filtering fusions arising from hairpin structures (remaining=597546)
[2026-06-08T07:48:54] Filtering reads with a mismatch p-value <=0.01 (remaining=209462)
[2026-06-08T07:48:55] Filtering reads with low entropy (k-mer content >=60%) (remaining=62838)
[2026-06-08T07:48:57] Finding fusions and counting supporting reads (total=61192)
[2026-06-08T07:49:01] Merging adjacent fusion breakpoints (remaining=60962)
[2026-06-08T07:49:01] Filtering multi-mapping fusions by alignment score and read support (remaining=27905)
[2026-06-08T07:49:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:49:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=27504)
[2026-06-08T07:49:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=18733)
[2026-06-08T07:49:11] Filtering fusions with <2 supporting reads (remaining=812)
[2026-06-08T07:49:11] Filtering fusions with an e-value >=0.3 (remaining=270)
[2026-06-08T07:49:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=274)
[2026-06-08T07:49:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=240)
[2026-06-08T07:49:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=240)
[2026-06-08T07:49:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=238)
[2026-06-08T07:49:14] Searching for fusions with spliced split reads (remaining=266)
[2026-06-08T07:49:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=213)
[2026-06-08T07:49:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=210)
[2026-06-08T07:49:16] Searching for fusions with >=4 spliced events (remaining=217)
[2026-06-08T07:49:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=71)
[2026-06-08T07:49:29] Filtering fusions with anchors <=23nt (remaining=53)
[2026-06-08T07:49:29] Filtering end-to-end fusions with low support (remaining=53)
[2026-06-08T07:49:30] Filtering fusions with no coverage around the breakpoints (remaining=48)
[2026-06-08T07:49:30] Indexing gene sequences 
[2026-06-08T07:49:31] Filtering genes with >=30% identity (remaining=25)
[2026-06-08T07:49:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=17)
[2026-06-08T07:49:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=14)
[2026-06-08T07:49:32] Searching for additional isoforms (remaining=19)
[2026-06-08T07:49:32] Assigning confidence scores to events 
[2026-06-08T07:49:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:49:33] Writing fusions to file '659_bCu-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:49:33] Writing discarded fusions to file '659_bCu-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:49:40] Freeing resources
[2026-06-08T07:49:50] Done (elapsed time=00:04:04, CPU time=00:04:02, peak memory=7.15gb)