[2026-06-08T07:53:01] Launching Arriba 2.4.0
[2026-06-08T07:53:01] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:53:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:53:21] Reading chimeric alignments from '1173_RGW_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=14673354)
[2026-06-08T07:57:54] Marking multi-mapping alignments (marked=11995957)
[2026-06-08T07:57:59] Detecting strandedness (no)
[2026-06-08T07:57:59] Annotating alignments 
[2026-06-08T07:58:55] Filtering duplicates (remaining=3372855)
[2026-06-08T07:59:04] 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=2556704)
[2026-06-08T07:59:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2556704)
[2026-06-08T07:59:10] Filtering viral contigs with expression lower than the top 5 (remaining=2556704)
[2026-06-08T07:59:16] Filtering viral contigs with less than 5% coverage (remaining=2556704)
[2026-06-08T07:59:19] Estimating fragment length (mate gap mean=-65.3909, mate gap stddev=26.5724, read length mean=99.5445)
[2026-06-08T07:59:19] Filtering read-through fragments with a distance <=10000bp (remaining=2486320)
[2026-06-08T07:59:22] Filtering inconsistently clipped mates (remaining=2392321)
[2026-06-08T07:59:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2288652)
[2026-06-08T07:59:28] Filtering fragments with small insert size (remaining=2285245)
[2026-06-08T07:59:31] Filtering alignments with long gaps (remaining=2285245)
[2026-06-08T07:59:34] Filtering fragments with both mates in the same gene (remaining=2284194)
[2026-06-08T07:59:37] Filtering fusions arising from hairpin structures (remaining=2113621)
[2026-06-08T07:59:40] Filtering reads with a mismatch p-value <=0.01 (remaining=630828)
[2026-06-08T07:59:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=208277)
[2026-06-08T07:59:53] Finding fusions and counting supporting reads (total=177142)
[2026-06-08T08:00:10] Merging adjacent fusion breakpoints (remaining=174122)
[2026-06-08T08:00:11] Filtering multi-mapping fusions by alignment score and read support (remaining=75212)
[2026-06-08T08:00:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:00:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=74164)
[2026-06-08T08:00:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=50961)
[2026-06-08T08:00:59] Filtering fusions with <2 supporting reads (remaining=2238)
[2026-06-08T08:00:59] Filtering fusions with an e-value >=0.3 (remaining=549)
[2026-06-08T08:00:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=639)
[2026-06-08T08:01:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=545)
[2026-06-08T08:01:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=545)
[2026-06-08T08:01:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=541)
[2026-06-08T08:01:10] Searching for fusions with spliced split reads (remaining=563)
[2026-06-08T08:01:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=437)
[2026-06-08T08:01:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=434)
[2026-06-08T08:01:16] Searching for fusions with >=4 spliced events (remaining=445)
[2026-06-08T08:01:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=131)
[2026-06-08T08:01:37] Filtering fusions with anchors <=23nt (remaining=115)
[2026-06-08T08:01:38] Filtering end-to-end fusions with low support (remaining=108)
[2026-06-08T08:01:38] Filtering fusions with no coverage around the breakpoints (remaining=102)
[2026-06-08T08:01:38] Indexing gene sequences 
[2026-06-08T08:01:40] Filtering genes with >=30% identity (remaining=41)
[2026-06-08T08:01:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=19)
[2026-06-08T08:01:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=19)
[2026-06-08T08:01:42] Searching for additional isoforms (remaining=19)
[2026-06-08T08:01:42] Assigning confidence scores to events 
[2026-06-08T08:01:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:01:44] Writing fusions to file '1173_RGW_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:01:45] Writing discarded fusions to file '1173_RGW_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:02:01] Freeing resources
[2026-06-08T08:02:27] Done (elapsed time=00:09:26, CPU time=00:09:24, peak memory=18.8gb)