[2026-06-08T08:33:29] Launching Arriba 2.4.0
[2026-06-08T08:33:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:33:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:33:42] Reading chimeric alignments from '1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=18977549)
[2026-06-08T08:41:19] Marking multi-mapping alignments (marked=14006902)
[2026-06-08T08:41:27] Detecting strandedness (reverse)
[2026-06-08T08:41:27] Assigning strands to alignments 
[2026-06-08T08:41:31] Annotating alignments 
[2026-06-08T08:42:33] Filtering duplicates (remaining=8852805)
[2026-06-08T08:42:45] 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=7844824)
[2026-06-08T08:42:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7844824)
[2026-06-08T08:42:53] Filtering viral contigs with expression lower than the top 5 (remaining=7844824)
[2026-06-08T08:43:02] Filtering viral contigs with less than 5% coverage (remaining=7844824)
[2026-06-08T08:43:07] Estimating fragment length (mate gap mean=-75.8847, mate gap stddev=27.2481, read length mean=112.758)
[2026-06-08T08:43:07] Filtering read-through fragments with a distance <=10000bp (remaining=7607423)
[2026-06-08T08:43:11] Filtering inconsistently clipped mates (remaining=7403479)
[2026-06-08T08:43:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7242777)
[2026-06-08T08:43:22] Filtering fragments with small insert size (remaining=7240434)
[2026-06-08T08:43:26] Filtering alignments with long gaps (remaining=7240433)
[2026-06-08T08:43:30] Filtering fragments with both mates in the same gene (remaining=7238875)
[2026-06-08T08:43:34] Filtering fusions arising from hairpin structures (remaining=6779876)
[2026-06-08T08:43:38] Filtering reads with a mismatch p-value <=0.01 (remaining=2711292)
[2026-06-08T08:43:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=957072)
[2026-06-08T08:44:10] Finding fusions and counting supporting reads (total=833994)
[2026-06-08T08:44:39] Merging adjacent fusion breakpoints (remaining=822783)
[2026-06-08T08:44:41] Filtering multi-mapping fusions by alignment score and read support (remaining=400066)
[2026-06-08T08:45:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=398925)
[2026-06-08T08:45:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=297078)
[2026-06-08T08:45:53] Filtering fusions with <2 supporting reads (remaining=13576)
[2026-06-08T08:45:54] Filtering fusions with an e-value >=0.3 (remaining=2768)
[2026-06-08T08:45:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2923)
[2026-06-08T08:46:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2828)
[2026-06-08T08:46:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2828)
[2026-06-08T08:46:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2827)
[2026-06-08T08:46:14] Searching for fusions with spliced split reads (remaining=2874)
[2026-06-08T08:46:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=2066)
[2026-06-08T08:46:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2050)
[2026-06-08T08:46:26] Searching for fusions with >=4 spliced events (remaining=2395)
[2026-06-08T08:46:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1050)
[2026-06-08T08:46:41] Filtering fusions with anchors <=23nt (remaining=866)
[2026-06-08T08:46:42] Filtering end-to-end fusions with low support (remaining=838)
[2026-06-08T08:46:43] Filtering fusions with no coverage around the breakpoints (remaining=827)
[2026-06-08T08:46:44] Indexing gene sequences 
[2026-06-08T08:46:49] Filtering genes with >=30% identity (remaining=268)
[2026-06-08T08:46:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=117)
[2026-06-08T08:46:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=86)
[2026-06-08T08:46:56] Searching for additional isoforms (remaining=106)
[2026-06-08T08:46:58] Assigning confidence scores to events 
[2026-06-08T08:47:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:02] Writing fusions to file '1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:03] Writing discarded fusions to file '1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:46] Freeing resources
[2026-06-08T08:48:14] Done (elapsed time=00:14:45, CPU time=00:14:43, peak memory=23.2gb)