[2026-06-08T07:18:11] Launching Arriba 2.4.0
[2026-06-08T07:18:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:18:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:18:35] Reading chimeric alignments from '659_dQk-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=35404)
[2026-06-08T07:18:35] Marking multi-mapping alignments (marked=32462)
[2026-06-08T07:18:35] Detecting strandedness (no)
[2026-06-08T07:18:35] Annotating alignments 
[2026-06-08T07:18:36] Filtering duplicates (remaining=16690)
[2026-06-08T07:18:36] 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=13823)
[2026-06-08T07:18:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=13823)
[2026-06-08T07:18:36] Filtering viral contigs with expression lower than the top 5 (remaining=13823)
[2026-06-08T07:18:36] Filtering viral contigs with less than 5% coverage (remaining=13823)
[2026-06-08T07:18:36] Estimating fragment length (mate gap mean=-25.422, mate gap stddev=17.6871, read length mean=64.3335)
[2026-06-08T07:18:36] Filtering read-through fragments with a distance <=10000bp (remaining=13815)
[2026-06-08T07:18:36] Filtering inconsistently clipped mates (remaining=12622)
[2026-06-08T07:18:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=11853)
[2026-06-08T07:18:36] Filtering fragments with small insert size (remaining=11846)
[2026-06-08T07:18:36] Filtering alignments with long gaps (remaining=11846)
[2026-06-08T07:18:36] Filtering fragments with both mates in the same gene (remaining=11796)
[2026-06-08T07:18:36] Filtering fusions arising from hairpin structures (remaining=10798)
[2026-06-08T07:18:36] Filtering reads with a mismatch p-value <=0.01 (remaining=472)
[2026-06-08T07:18:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=64)
[2026-06-08T07:18:36] Finding fusions and counting supporting reads (total=59)
[2026-06-08T07:18:36] Merging adjacent fusion breakpoints (remaining=59)
[2026-06-08T07:18:36] Filtering multi-mapping fusions by alignment score and read support (remaining=44)
[2026-06-08T07:18:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:18:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=43)
[2026-06-08T07:18:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=43)
[2026-06-08T07:18:36] Filtering fusions with <2 supporting reads (remaining=2)
[2026-06-08T07:18:36] Filtering fusions with an e-value >=0.3 (remaining=2)
[2026-06-08T07:18:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2)
[2026-06-08T07:18:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=0)
[2026-06-08T07:18:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=0)
[2026-06-08T07:18:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=0)
[2026-06-08T07:18:36] Searching for fusions with spliced split reads (remaining=0)
[2026-06-08T07:18:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:18:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=0)
[2026-06-08T07:18:36] Searching for fusions with >=4 spliced events (remaining=0)
[2026-06-08T07:18:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=0)
[2026-06-08T07:18:54] Filtering fusions with anchors <=23nt (remaining=0)
[2026-06-08T07:18:54] Filtering end-to-end fusions with low support (remaining=0)
[2026-06-08T07:18:54] Filtering fusions with no coverage around the breakpoints (remaining=0)
[2026-06-08T07:18:54] Indexing gene sequences 
[2026-06-08T07:18:54] Filtering genes with >=30% identity (remaining=0)
[2026-06-08T07:18:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-08T07:18:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:18:54] Searching for additional isoforms (remaining=0)
[2026-06-08T07:18:54] Assigning confidence scores to events 
[2026-06-08T07:18:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:18:54] Writing fusions to file '659_dQk-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:18:54] Writing discarded fusions to file '659_dQk-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:18:54] Freeing resources
[2026-06-08T07:18:55] Done (elapsed time=00:00:44, CPU time=00:00:42, peak memory=4.11gb)