[2026-06-08T08:31:30] Launching Arriba 2.4.0
[2026-06-08T08:31:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:49] Reading chimeric alignments from '1173_LV7_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=15794048)
[2026-06-08T08:40:36] Marking multi-mapping alignments (marked=10526893)
[2026-06-08T08:40:42] Detecting strandedness (reverse)
[2026-06-08T08:40:42] Assigning strands to alignments 
[2026-06-08T08:40:45] Annotating alignments 
[2026-06-08T08:41:37] Filtering duplicates (remaining=10415796)
[2026-06-08T08:41:48] 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=9751929)
[2026-06-08T08:41:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9751929)
[2026-06-08T08:41:54] Filtering viral contigs with expression lower than the top 5 (remaining=9751929)
[2026-06-08T08:42:01] Filtering viral contigs with less than 5% coverage (remaining=9751929)
[2026-06-08T08:42:05] Estimating fragment length (mate gap mean=-80.9298, mate gap stddev=26.4328, read length mean=122.932)
[2026-06-08T08:42:05] Filtering read-through fragments with a distance <=10000bp (remaining=9476227)
[2026-06-08T08:42:08] Filtering inconsistently clipped mates (remaining=9276942)
[2026-06-08T08:42:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9154560)
[2026-06-08T08:42:17] Filtering fragments with small insert size (remaining=9152842)
[2026-06-08T08:42:21] Filtering alignments with long gaps (remaining=9152842)
[2026-06-08T08:42:24] Filtering fragments with both mates in the same gene (remaining=9151108)
[2026-06-08T08:42:27] Filtering fusions arising from hairpin structures (remaining=8626840)
[2026-06-08T08:42:31] Filtering reads with a mismatch p-value <=0.01 (remaining=4310414)
[2026-06-08T08:42:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=1928867)
[2026-06-08T08:43:12] Finding fusions and counting supporting reads (total=1803505)
[2026-06-08T08:43:38] Merging adjacent fusion breakpoints (remaining=1793991)
[2026-06-08T08:43:41] Filtering multi-mapping fusions by alignment score and read support (remaining=1027662)
[2026-06-08T08:44:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1026479)
[2026-06-08T08:44:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=864891)
[2026-06-08T08:44:42] Filtering fusions with <2 supporting reads (remaining=22822)
[2026-06-08T08:44:44] Filtering fusions with an e-value >=0.3 (remaining=3590)
[2026-06-08T08:44:45] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3710)
[2026-06-08T08:44:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3620)
[2026-06-08T08:44:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3620)
[2026-06-08T08:44:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3612)
[2026-06-08T08:45:02] Searching for fusions with spliced split reads (remaining=3713)
[2026-06-08T08:45:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=2652)
[2026-06-08T08:45:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2628)
[2026-06-08T08:45:14] Searching for fusions with >=4 spliced events (remaining=3211)
[2026-06-08T08:45:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1439)
[2026-06-08T08:45:31] Filtering fusions with anchors <=23nt (remaining=1250)
[2026-06-08T08:45:32] Filtering end-to-end fusions with low support (remaining=1213)
[2026-06-08T08:45:34] Filtering fusions with no coverage around the breakpoints (remaining=1193)
[2026-06-08T08:45:35] Indexing gene sequences 
[2026-06-08T08:45:41] Filtering genes with >=30% identity (remaining=371)
[2026-06-08T08:45:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=191)
[2026-06-08T08:45:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=155)
[2026-06-08T08:45:51] Searching for additional isoforms (remaining=189)
[2026-06-08T08:45:53] Assigning confidence scores to events 
[2026-06-08T08:45:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:59] Writing fusions to file '1173_LV7_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:46:01] Writing discarded fusions to file '1173_LV7_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:58] Freeing resources
[2026-06-08T08:47:31] Done (elapsed time=00:16:01, CPU time=00:16:00, peak memory=20.3gb)