[2026-06-08T08:24:38] Launching Arriba 2.4.0
[2026-06-08T08:24:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:24:53] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s34.Aligned.sortedByCoord.out.bam' (total=11905887)
[2026-06-08T08:33:42] Marking multi-mapping alignments (marked=8256601)
[2026-06-08T08:33:51] Detecting strandedness (reverse)
[2026-06-08T08:33:51] Assigning strands to alignments 
[2026-06-08T08:33:56] Annotating alignments 
[2026-06-08T08:35:08] Filtering duplicates (remaining=5979032)
[2026-06-08T08:35:19] 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=5321109)
[2026-06-08T08:35:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5321109)
[2026-06-08T08:35:27] Filtering viral contigs with expression lower than the top 5 (remaining=5321109)
[2026-06-08T08:35:36] Filtering viral contigs with less than 5% coverage (remaining=5321109)
[2026-06-08T08:35:40] Estimating fragment length (mate gap mean=-82.5936, mate gap stddev=31.9619, read length mean=130.179)
[2026-06-08T08:35:40] Filtering read-through fragments with a distance <=10000bp (remaining=5098909)
[2026-06-08T08:35:44] Filtering inconsistently clipped mates (remaining=5012615)
[2026-06-08T08:35:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4551356)
[2026-06-08T08:35:56] Filtering fragments with small insert size (remaining=4550402)
[2026-06-08T08:36:00] Filtering alignments with long gaps (remaining=4550402)
[2026-06-08T08:36:04] Filtering fragments with both mates in the same gene (remaining=4548501)
[2026-06-08T08:36:08] Filtering fusions arising from hairpin structures (remaining=4274770)
[2026-06-08T08:36:13] Filtering reads with a mismatch p-value <=0.01 (remaining=1761092)
[2026-06-08T08:36:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=898525)
[2026-06-08T08:36:45] Finding fusions and counting supporting reads (total=795166)
[2026-06-08T08:37:13] Merging adjacent fusion breakpoints (remaining=790803)
[2026-06-08T08:37:16] Filtering multi-mapping fusions by alignment score and read support (remaining=443845)
[2026-06-08T08:38:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:38:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=440916)
[2026-06-08T08:38:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=310794)
[2026-06-08T08:38:26] Filtering fusions with <2 supporting reads (remaining=21605)
[2026-06-08T08:38:27] Filtering fusions with an e-value >=0.3 (remaining=5316)
[2026-06-08T08:38:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5342)
[2026-06-08T08:38:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5118)
[2026-06-08T08:38:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5131)
[2026-06-08T08:38:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4019)
[2026-06-08T08:38:46] Searching for fusions with spliced split reads (remaining=4111)
[2026-06-08T08:38:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=2475)
[2026-06-08T08:38:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2442)
[2026-06-08T08:38:59] Searching for fusions with >=4 spliced events (remaining=2967)
[2026-06-08T08:39:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1120)
[2026-06-08T08:39:20] Filtering fusions with anchors <=23nt (remaining=831)
[2026-06-08T08:39:21] Filtering end-to-end fusions with low support (remaining=808)
[2026-06-08T08:39:22] Filtering fusions with no coverage around the breakpoints (remaining=796)
[2026-06-08T08:39:23] Indexing gene sequences 
[2026-06-08T08:39:29] Filtering genes with >=30% identity (remaining=191)
[2026-06-08T08:39:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=85)
[2026-06-08T08:39:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=82)
[2026-06-08T08:39:37] Searching for additional isoforms (remaining=102)
[2026-06-08T08:39:39] Assigning confidence scores to events 
[2026-06-08T08:39:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:39:44] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s34.arriba.fusions.tsv' 
[2026-06-08T08:39:46] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s34.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:42] Freeing resources
[2026-06-08T08:41:31] Done (elapsed time=00:16:53, CPU time=00:16:51, peak memory=16.9gb)