[2026-06-08T08:23:20] Launching Arriba 2.4.0
[2026-06-08T08:23:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:33] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:36] Reading chimeric alignments from '1173_GFO_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=15332181)
[2026-06-08T08:29:26] Marking multi-mapping alignments (marked=10835102)
[2026-06-08T08:29:32] Detecting strandedness (reverse)
[2026-06-08T08:29:32] Assigning strands to alignments 
[2026-06-08T08:29:34] Annotating alignments 
[2026-06-08T08:30:14] Filtering duplicates (remaining=6394448)
[2026-06-08T08:30:22] 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=5930839)
[2026-06-08T08:30:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5930839)
[2026-06-08T08:30:27] Filtering viral contigs with expression lower than the top 5 (remaining=5930839)
[2026-06-08T08:30:33] Filtering viral contigs with less than 5% coverage (remaining=5930839)
[2026-06-08T08:30:36] Estimating fragment length (mate gap mean=-82.1856, mate gap stddev=27.7344, read length mean=121.566)
[2026-06-08T08:30:36] Filtering read-through fragments with a distance <=10000bp (remaining=5696400)
[2026-06-08T08:30:39] Filtering inconsistently clipped mates (remaining=5535153)
[2026-06-08T08:30:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5415296)
[2026-06-08T08:30:46] Filtering fragments with small insert size (remaining=5413825)
[2026-06-08T08:30:49] Filtering alignments with long gaps (remaining=5413825)
[2026-06-08T08:30:52] Filtering fragments with both mates in the same gene (remaining=5412877)
[2026-06-08T08:30:55] Filtering fusions arising from hairpin structures (remaining=5053870)
[2026-06-08T08:30:58] Filtering reads with a mismatch p-value <=0.01 (remaining=2094245)
[2026-06-08T08:31:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=724333)
[2026-06-08T08:31:21] Finding fusions and counting supporting reads (total=627939)
[2026-06-08T08:31:39] Merging adjacent fusion breakpoints (remaining=621470)
[2026-06-08T08:31:41] Filtering multi-mapping fusions by alignment score and read support (remaining=328067)
[2026-06-08T08:32:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=327030)
[2026-06-08T08:32:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=229486)
[2026-06-08T08:32:27] Filtering fusions with <2 supporting reads (remaining=11151)
[2026-06-08T08:32:28] Filtering fusions with an e-value >=0.3 (remaining=2543)
[2026-06-08T08:32:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2664)
[2026-06-08T08:32:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2597)
[2026-06-08T08:32:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2597)
[2026-06-08T08:32:35] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2591)
[2026-06-08T08:32:40] Searching for fusions with spliced split reads (remaining=2638)
[2026-06-08T08:32:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=1954)
[2026-06-08T08:32:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1931)
[2026-06-08T08:32:48] Searching for fusions with >=4 spliced events (remaining=2160)
[2026-06-08T08:32:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=799)
[2026-06-08T08:33:02] Filtering fusions with anchors <=23nt (remaining=683)
[2026-06-08T08:33:03] Filtering end-to-end fusions with low support (remaining=650)
[2026-06-08T08:33:03] Filtering fusions with no coverage around the breakpoints (remaining=632)
[2026-06-08T08:33:04] Indexing gene sequences 
[2026-06-08T08:33:07] Filtering genes with >=30% identity (remaining=228)
[2026-06-08T08:33:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=125)
[2026-06-08T08:33:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=115)
[2026-06-08T08:33:12] Searching for additional isoforms (remaining=130)
[2026-06-08T08:33:13] Assigning confidence scores to events 
[2026-06-08T08:33:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:33:16] Writing fusions to file '1173_GFO_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:33:17] Writing discarded fusions to file '1173_GFO_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:33:41] Freeing resources
[2026-06-08T08:34:02] Done (elapsed time=00:10:42, CPU time=00:10:41, peak memory=19.5gb)