[2026-06-08T08:19:17] Launching Arriba 2.4.0
[2026-06-08T08:19:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:38] Reading chimeric alignments from '1173_KTN_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=10351866)
[2026-06-08T08:25:52] Marking multi-mapping alignments (marked=7017099)
[2026-06-08T08:25:56] Detecting strandedness (reverse)
[2026-06-08T08:25:56] Assigning strands to alignments 
[2026-06-08T08:25:59] Annotating alignments 
[2026-06-08T08:26:35] Filtering duplicates (remaining=6078827)
[2026-06-08T08:26:43] 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=5750541)
[2026-06-08T08:26:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5750541)
[2026-06-08T08:26:47] Filtering viral contigs with expression lower than the top 5 (remaining=5750541)
[2026-06-08T08:26:52] Filtering viral contigs with less than 5% coverage (remaining=5750541)
[2026-06-08T08:26:54] Estimating fragment length (mate gap mean=-79.8664, mate gap stddev=26.1729, read length mean=117.929)
[2026-06-08T08:26:54] Filtering read-through fragments with a distance <=10000bp (remaining=5540748)
[2026-06-08T08:26:57] Filtering inconsistently clipped mates (remaining=5433337)
[2026-06-08T08:26:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5316379)
[2026-06-08T08:27:03] Filtering fragments with small insert size (remaining=5315276)
[2026-06-08T08:27:05] Filtering alignments with long gaps (remaining=5315276)
[2026-06-08T08:27:07] Filtering fragments with both mates in the same gene (remaining=5314252)
[2026-06-08T08:27:09] Filtering fusions arising from hairpin structures (remaining=5049368)
[2026-06-08T08:27:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2188807)
[2026-06-08T08:27:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=859011)
[2026-06-08T08:27:36] Finding fusions and counting supporting reads (total=746763)
[2026-06-08T08:27:54] Merging adjacent fusion breakpoints (remaining=740326)
[2026-06-08T08:27:55] Filtering multi-mapping fusions by alignment score and read support (remaining=414381)
[2026-06-08T08:28:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=413614)
[2026-06-08T08:28:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=321043)
[2026-06-08T08:28:38] Filtering fusions with <2 supporting reads (remaining=17239)
[2026-06-08T08:28:39] Filtering fusions with an e-value >=0.3 (remaining=3282)
[2026-06-08T08:28:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3356)
[2026-06-08T08:28:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3313)
[2026-06-08T08:28:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3313)
[2026-06-08T08:28:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3306)
[2026-06-08T08:28:51] Searching for fusions with spliced split reads (remaining=3392)
[2026-06-08T08:28:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=2421)
[2026-06-08T08:28:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2395)
[2026-06-08T08:28:59] Searching for fusions with >=4 spliced events (remaining=2854)
[2026-06-08T08:29:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1393)
[2026-06-08T08:29:15] Filtering fusions with anchors <=23nt (remaining=1163)
[2026-06-08T08:29:15] Filtering end-to-end fusions with low support (remaining=1131)
[2026-06-08T08:29:16] Filtering fusions with no coverage around the breakpoints (remaining=1089)
[2026-06-08T08:29:17] Indexing gene sequences 
[2026-06-08T08:29:22] Filtering genes with >=30% identity (remaining=498)
[2026-06-08T08:29:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=351)
[2026-06-08T08:29:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=215)
[2026-06-08T08:29:40] Searching for additional isoforms (remaining=296)
[2026-06-08T08:29:41] Assigning confidence scores to events 
[2026-06-08T08:29:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:45] Writing fusions to file '1173_KTN_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:29:48] Writing discarded fusions to file '1173_KTN_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:30:25] Freeing resources
[2026-06-08T08:30:44] Done (elapsed time=00:11:27, CPU time=00:11:26, peak memory=14.7gb)