[2026-06-08T08:27:27] Launching Arriba 2.4.0
[2026-06-08T08:27:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:43] Reading chimeric alignments from '1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=14026289)
[2026-06-08T08:34:12] Marking multi-mapping alignments (marked=9476660)
[2026-06-08T08:34:17] Detecting strandedness (reverse)
[2026-06-08T08:34:17] Assigning strands to alignments 
[2026-06-08T08:34:20] Annotating alignments 
[2026-06-08T08:34:59] Filtering duplicates (remaining=9741911)
[2026-06-08T08:35:08] 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=9122031)
[2026-06-08T08:35:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9122031)
[2026-06-08T08:35:13] Filtering viral contigs with expression lower than the top 5 (remaining=9122031)
[2026-06-08T08:35:18] Filtering viral contigs with less than 5% coverage (remaining=9122031)
[2026-06-08T08:35:21] Estimating fragment length (mate gap mean=-80.6353, mate gap stddev=26.0573, read length mean=123.011)
[2026-06-08T08:35:21] Filtering read-through fragments with a distance <=10000bp (remaining=8835950)
[2026-06-08T08:35:23] Filtering inconsistently clipped mates (remaining=8709247)
[2026-06-08T08:35:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8542560)
[2026-06-08T08:35:32] Filtering fragments with small insert size (remaining=8541577)
[2026-06-08T08:35:34] Filtering alignments with long gaps (remaining=8541576)
[2026-06-08T08:35:37] Filtering fragments with both mates in the same gene (remaining=8539993)
[2026-06-08T08:35:39] Filtering fusions arising from hairpin structures (remaining=8223697)
[2026-06-08T08:35:42] Filtering reads with a mismatch p-value <=0.01 (remaining=4388380)
[2026-06-08T08:36:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=2373245)
[2026-06-08T08:36:16] Finding fusions and counting supporting reads (total=2165759)
[2026-06-08T08:36:38] Merging adjacent fusion breakpoints (remaining=2156280)
[2026-06-08T08:36:41] Filtering multi-mapping fusions by alignment score and read support (remaining=1176275)
[2026-06-08T08:37:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:37:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1175245)
[2026-06-08T08:37:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1064016)
[2026-06-08T08:37:33] Filtering fusions with <2 supporting reads (remaining=27451)
[2026-06-08T08:37:34] Filtering fusions with an e-value >=0.3 (remaining=3860)
[2026-06-08T08:37:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3955)
[2026-06-08T08:37:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3880)
[2026-06-08T08:37:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3884)
[2026-06-08T08:37:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3776)
[2026-06-08T08:37:51] Searching for fusions with spliced split reads (remaining=3909)
[2026-06-08T08:37:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=2864)
[2026-06-08T08:38:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2828)
[2026-06-08T08:38:01] Searching for fusions with >=4 spliced events (remaining=3362)
[2026-06-08T08:38:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1332)
[2026-06-08T08:38:16] Filtering fusions with anchors <=23nt (remaining=1113)
[2026-06-08T08:38:17] Filtering end-to-end fusions with low support (remaining=1086)
[2026-06-08T08:38:18] Filtering fusions with no coverage around the breakpoints (remaining=1053)
[2026-06-08T08:38:19] Indexing gene sequences 
[2026-06-08T08:38:24] Filtering genes with >=30% identity (remaining=317)
[2026-06-08T08:38:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=151)
[2026-06-08T08:38:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=148)
[2026-06-08T08:38:35] Searching for additional isoforms (remaining=188)
[2026-06-08T08:38:37] Assigning confidence scores to events 
[2026-06-08T08:38:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:38:42] Writing fusions to file '1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:38:43] Writing discarded fusions to file '1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:39:24] Freeing resources
[2026-06-08T08:39:44] Done (elapsed time=00:12:17, CPU time=00:12:16, peak memory=18.8gb)