[2026-06-08T08:11:17] Launching Arriba 2.4.0
[2026-06-08T08:11:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:11:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:11:30] Reading chimeric alignments from '1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=11804111)
[2026-06-08T08:16:31] Marking multi-mapping alignments (marked=8307783)
[2026-06-08T08:16:36] Detecting strandedness (no)
[2026-06-08T08:16:36] Annotating alignments 
[2026-06-08T08:17:18] Filtering duplicates (remaining=7503481)
[2026-06-08T08:17:27] 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=6944975)
[2026-06-08T08:17:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6944975)
[2026-06-08T08:17:33] Filtering viral contigs with expression lower than the top 5 (remaining=6944975)
[2026-06-08T08:17:38] Filtering viral contigs with less than 5% coverage (remaining=6944975)
[2026-06-08T08:17:41] Estimating fragment length (mate gap mean=-78.4638, mate gap stddev=26.5133, read length mean=116.886)
[2026-06-08T08:17:41] Filtering read-through fragments with a distance <=10000bp (remaining=6676179)
[2026-06-08T08:17:43] Filtering inconsistently clipped mates (remaining=6563417)
[2026-06-08T08:17:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6445421)
[2026-06-08T08:17:50] Filtering fragments with small insert size (remaining=6444161)
[2026-06-08T08:17:52] Filtering alignments with long gaps (remaining=6444160)
[2026-06-08T08:17:55] Filtering fragments with both mates in the same gene (remaining=6443069)
[2026-06-08T08:17:57] Filtering fusions arising from hairpin structures (remaining=6194925)
[2026-06-08T08:18:00] Filtering reads with a mismatch p-value <=0.01 (remaining=2682553)
[2026-06-08T08:18:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=1114684)
[2026-06-08T08:18:25] Finding fusions and counting supporting reads (total=985748)
[2026-06-08T08:18:43] Merging adjacent fusion breakpoints (remaining=978081)
[2026-06-08T08:18:45] Filtering multi-mapping fusions by alignment score and read support (remaining=512452)
[2026-06-08T08:19:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:19:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=511581)
[2026-06-08T08:19:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=407078)
[2026-06-08T08:19:33] Filtering fusions with <2 supporting reads (remaining=20288)
[2026-06-08T08:19:34] Filtering fusions with an e-value >=0.3 (remaining=3665)
[2026-06-08T08:19:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3729)
[2026-06-08T08:19:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3662)
[2026-06-08T08:19:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3663)
[2026-06-08T08:19:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3662)
[2026-06-08T08:19:49] Searching for fusions with spliced split reads (remaining=3723)
[2026-06-08T08:19:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=2746)
[2026-06-08T08:19:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2722)
[2026-06-08T08:19:58] Searching for fusions with >=4 spliced events (remaining=3279)
[2026-06-08T08:20:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1458)
[2026-06-08T08:20:12] Filtering fusions with anchors <=23nt (remaining=1229)
[2026-06-08T08:20:13] Filtering end-to-end fusions with low support (remaining=1202)
[2026-06-08T08:20:14] Filtering fusions with no coverage around the breakpoints (remaining=1177)
[2026-06-08T08:20:15] Indexing gene sequences 
[2026-06-08T08:20:20] Filtering genes with >=30% identity (remaining=374)
[2026-06-08T08:20:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=132)
[2026-06-08T08:20:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-08T08:20:29] Searching for additional isoforms (remaining=152)
[2026-06-08T08:20:31] Assigning confidence scores to events 
[2026-06-08T08:20:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:20:35] Writing fusions to file '1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:20:37] Writing discarded fusions to file '1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:21:11] Freeing resources
[2026-06-08T08:21:29] Done (elapsed time=00:10:12, CPU time=00:10:11, peak memory=16.2gb)