[2026-06-08T07:29:53] Launching Arriba 2.4.0
[2026-06-08T07:29:53] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:30:06] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:30:13] Reading chimeric alignments from '1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=234433)
[2026-06-08T07:30:22] Marking multi-mapping alignments (marked=176510)
[2026-06-08T07:30:22] Detecting strandedness (no)
[2026-06-08T07:30:22] Annotating alignments 
[2026-06-08T07:30:23] Filtering duplicates (remaining=167828)
[2026-06-08T07:30:23] 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=151357)
[2026-06-08T07:30:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=151357)
[2026-06-08T07:30:23] Filtering viral contigs with expression lower than the top 5 (remaining=151357)
[2026-06-08T07:30:23] Filtering viral contigs with less than 5% coverage (remaining=151357)
[2026-06-08T07:30:24] Estimating fragment length (mate gap mean=-68.4234, mate gap stddev=27.1211, read length mean=104.789)
[2026-06-08T07:30:24] Filtering read-through fragments with a distance <=10000bp (remaining=147833)
[2026-06-08T07:30:24] Filtering inconsistently clipped mates (remaining=142495)
[2026-06-08T07:30:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=138398)
[2026-06-08T07:30:24] Filtering fragments with small insert size (remaining=138322)
[2026-06-08T07:30:24] Filtering alignments with long gaps (remaining=138322)
[2026-06-08T07:30:24] Filtering fragments with both mates in the same gene (remaining=138236)
[2026-06-08T07:30:24] Filtering fusions arising from hairpin structures (remaining=129403)
[2026-06-08T07:30:24] Filtering reads with a mismatch p-value <=0.01 (remaining=49954)
[2026-06-08T07:30:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=12327)
[2026-06-08T07:30:25] Finding fusions and counting supporting reads (total=12032)
[2026-06-08T07:30:25] Merging adjacent fusion breakpoints (remaining=11988)
[2026-06-08T07:30:25] Filtering multi-mapping fusions by alignment score and read support (remaining=6426)
[2026-06-08T07:30:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:30:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=6355)
[2026-06-08T07:30:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=4405)
[2026-06-08T07:30:26] Filtering fusions with <2 supporting reads (remaining=188)
[2026-06-08T07:30:26] Filtering fusions with an e-value >=0.3 (remaining=138)
[2026-06-08T07:30:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=144)
[2026-06-08T07:30:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=144)
[2026-06-08T07:30:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=144)
[2026-06-08T07:30:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=134)
[2026-06-08T07:30:27] Searching for fusions with spliced split reads (remaining=137)
[2026-06-08T07:30:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=109)
[2026-06-08T07:30:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=108)
[2026-06-08T07:30:27] Searching for fusions with >=4 spliced events (remaining=108)
[2026-06-08T07:30:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=27)
[2026-06-08T07:30:43] Filtering fusions with anchors <=23nt (remaining=24)
[2026-06-08T07:30:43] Filtering end-to-end fusions with low support (remaining=20)
[2026-06-08T07:30:43] Filtering fusions with no coverage around the breakpoints (remaining=20)
[2026-06-08T07:30:43] Indexing gene sequences 
[2026-06-08T07:30:43] Filtering genes with >=30% identity (remaining=11)
[2026-06-08T07:30:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=11)
[2026-06-08T07:30:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=11)
[2026-06-08T07:30:43] Searching for additional isoforms (remaining=13)
[2026-06-08T07:30:43] Assigning confidence scores to events 
[2026-06-08T07:30:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:30:44] Writing fusions to file '1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:30:44] Writing discarded fusions to file '1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:30:45] Freeing resources
[2026-06-08T07:30:46] Done (elapsed time=00:00:53, CPU time=00:00:52, peak memory=4.31gb)