[2026-06-08T08:38:24] Launching Arriba 2.4.0
[2026-06-08T08:38:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:36] Reading chimeric alignments from '1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=18738742)
[2026-06-08T08:45:28] Marking multi-mapping alignments (marked=13732596)
[2026-06-08T08:45:35] Detecting strandedness (reverse)
[2026-06-08T08:45:35] Assigning strands to alignments 
[2026-06-08T08:45:38] Annotating alignments 
[2026-06-08T08:46:52] Filtering duplicates (remaining=6949351)
[2026-06-08T08:47:12] 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=6300410)
[2026-06-08T08:47:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6300410)
[2026-06-08T08:47:21] Filtering viral contigs with expression lower than the top 5 (remaining=6300410)
[2026-06-08T08:47:30] Filtering viral contigs with less than 5% coverage (remaining=6300410)
[2026-06-08T08:47:34] Estimating fragment length (mate gap mean=-77.3816, mate gap stddev=27.9781, read length mean=114.629)
[2026-06-08T08:47:34] Filtering read-through fragments with a distance <=10000bp (remaining=6109628)
[2026-06-08T08:47:37] Filtering inconsistently clipped mates (remaining=5949537)
[2026-06-08T08:47:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5834509)
[2026-06-08T08:47:46] Filtering fragments with small insert size (remaining=5832305)
[2026-06-08T08:47:51] Filtering alignments with long gaps (remaining=5832305)
[2026-06-08T08:47:54] Filtering fragments with both mates in the same gene (remaining=5831121)
[2026-06-08T08:47:58] Filtering fusions arising from hairpin structures (remaining=5475869)
[2026-06-08T08:48:02] Filtering reads with a mismatch p-value <=0.01 (remaining=2140211)
[2026-06-08T08:48:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=631401)
[2026-06-08T08:48:27] Finding fusions and counting supporting reads (total=544126)
[2026-06-08T08:48:53] Merging adjacent fusion breakpoints (remaining=538133)
[2026-06-08T08:48:54] Filtering multi-mapping fusions by alignment score and read support (remaining=271838)
[2026-06-08T08:49:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=270970)
[2026-06-08T08:49:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=186429)
[2026-06-08T08:49:57] Filtering fusions with <2 supporting reads (remaining=10373)
[2026-06-08T08:49:58] Filtering fusions with an e-value >=0.3 (remaining=2238)
[2026-06-08T08:49:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2350)
[2026-06-08T08:50:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2280)
[2026-06-08T08:50:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2280)
[2026-06-08T08:50:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2280)
[2026-06-08T08:50:14] Searching for fusions with spliced split reads (remaining=2329)
[2026-06-08T08:50:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=1693)
[2026-06-08T08:50:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1680)
[2026-06-08T08:50:23] Searching for fusions with >=4 spliced events (remaining=1937)
[2026-06-08T08:50:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=817)
[2026-06-08T08:50:37] Filtering fusions with anchors <=23nt (remaining=683)
[2026-06-08T08:50:38] Filtering end-to-end fusions with low support (remaining=654)
[2026-06-08T08:50:39] Filtering fusions with no coverage around the breakpoints (remaining=631)
[2026-06-08T08:50:39] Indexing gene sequences 
[2026-06-08T08:50:43] Filtering genes with >=30% identity (remaining=222)
[2026-06-08T08:50:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=109)
[2026-06-08T08:50:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=76)
[2026-06-08T08:50:48] Searching for additional isoforms (remaining=92)
[2026-06-08T08:50:50] Assigning confidence scores to events 
[2026-06-08T08:50:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:53] Writing fusions to file '1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:50:54] Writing discarded fusions to file '1173_G2E_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:27] Freeing resources
[2026-06-08T08:51:53] Done (elapsed time=00:13:29, CPU time=00:13:28, peak memory=22.6gb)