[2026-06-08T07:17:37] Launching Arriba 2.4.0
[2026-06-08T07:17:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:17:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:18:03] Reading chimeric alignments from '659_eKx-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=45081)
[2026-06-08T07:18:04] Marking multi-mapping alignments (marked=41388)
[2026-06-08T07:18:04] Detecting strandedness (no)
[2026-06-08T07:18:04] Annotating alignments 
[2026-06-08T07:18:04] Filtering duplicates (remaining=23868)
[2026-06-08T07:18:04] 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=19873)
[2026-06-08T07:18:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=19873)
[2026-06-08T07:18:04] Filtering viral contigs with expression lower than the top 5 (remaining=19873)
[2026-06-08T07:18:04] Filtering viral contigs with less than 5% coverage (remaining=19873)
[2026-06-08T07:18:05] Estimating fragment length (mate gap mean=-15.8891, mate gap stddev=1.77698, read length mean=55.2982)
[2026-06-08T07:18:05] Filtering read-through fragments with a distance <=10000bp (remaining=19864)
[2026-06-08T07:18:05] Filtering inconsistently clipped mates (remaining=18999)
[2026-06-08T07:18:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=18005)
[2026-06-08T07:18:05] Filtering fragments with small insert size (remaining=17903)
[2026-06-08T07:18:05] Filtering alignments with long gaps (remaining=17903)
[2026-06-08T07:18:05] Filtering fragments with both mates in the same gene (remaining=17805)
[2026-06-08T07:18:05] Filtering fusions arising from hairpin structures (remaining=17070)
[2026-06-08T07:18:05] Filtering reads with a mismatch p-value <=0.01 (remaining=496)
[2026-06-08T07:18:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=63)
[2026-06-08T07:18:05] Finding fusions and counting supporting reads (total=69)
[2026-06-08T07:18:05] Merging adjacent fusion breakpoints (remaining=60)
[2026-06-08T07:18:05] Filtering multi-mapping fusions by alignment score and read support (remaining=60)
[2026-06-08T07:18:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:18:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=60)
[2026-06-08T07:18:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=60)
[2026-06-08T07:18:05] Filtering fusions with <2 supporting reads (remaining=1)
[2026-06-08T07:18:05] Filtering fusions with an e-value >=0.3 (remaining=1)
[2026-06-08T07:18:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1)
[2026-06-08T07:18:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1)
[2026-06-08T07:18:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1)
[2026-06-08T07:18:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=0)
[2026-06-08T07:18:05] Searching for fusions with spliced split reads (remaining=0)
[2026-06-08T07:18:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:18:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=0)
[2026-06-08T07:18:05] Searching for fusions with >=4 spliced events (remaining=0)
[2026-06-08T07:18:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=0)
[2026-06-08T07:18:23] Filtering fusions with anchors <=23nt (remaining=0)
[2026-06-08T07:18:23] Filtering end-to-end fusions with low support (remaining=0)
[2026-06-08T07:18:23] Filtering fusions with no coverage around the breakpoints (remaining=0)
[2026-06-08T07:18:23] Indexing gene sequences 
[2026-06-08T07:18:23] Filtering genes with >=30% identity (remaining=0)
[2026-06-08T07:18:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-08T07:18:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:18:23] Searching for additional isoforms (remaining=0)
[2026-06-08T07:18:23] Assigning confidence scores to events 
[2026-06-08T07:18:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:18:23] Writing fusions to file '659_eKx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:18:23] Writing discarded fusions to file '659_eKx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:18:23] Freeing resources
[2026-06-08T07:18:24] Done (elapsed time=00:00:47, CPU time=00:00:46, peak memory=4.1gb)