[2026-06-08T08:48:08] Launching Arriba 2.4.0
[2026-06-08T08:48:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:21] Reading chimeric alignments from '659_cWx-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=11877916)
[2026-06-08T08:55:13] Marking multi-mapping alignments (marked=7684539)
[2026-06-08T08:55:17] Detecting strandedness (reverse)
[2026-06-08T08:55:17] Assigning strands to alignments 
[2026-06-08T08:55:19] Annotating alignments 
[2026-06-08T08:55:57] Filtering duplicates (remaining=3292134)
[2026-06-08T08:56:02] 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=3061165)
[2026-06-08T08:56:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3061165)
[2026-06-08T08:56:07] Filtering viral contigs with expression lower than the top 5 (remaining=3061165)
[2026-06-08T08:56:12] Filtering viral contigs with less than 5% coverage (remaining=3061165)
[2026-06-08T08:56:14] Estimating fragment length (mate gap mean=-85.2291, mate gap stddev=29.8923, read length mean=134.024)
[2026-06-08T08:56:14] Filtering read-through fragments with a distance <=10000bp (remaining=2935783)
[2026-06-08T08:56:17] Filtering inconsistently clipped mates (remaining=2890194)
[2026-06-08T08:56:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2728518)
[2026-06-08T08:56:22] Filtering fragments with small insert size (remaining=2728066)
[2026-06-08T08:56:24] Filtering alignments with long gaps (remaining=2728066)
[2026-06-08T08:56:26] Filtering fragments with both mates in the same gene (remaining=2727490)
[2026-06-08T08:56:29] Filtering fusions arising from hairpin structures (remaining=2636456)
[2026-06-08T08:56:31] Filtering reads with a mismatch p-value <=0.01 (remaining=1072895)
[2026-06-08T08:56:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=277917)
[2026-06-08T08:56:45] Finding fusions and counting supporting reads (total=248468)
[2026-06-08T08:56:59] Merging adjacent fusion breakpoints (remaining=246321)
[2026-06-08T08:57:00] Filtering multi-mapping fusions by alignment score and read support (remaining=136078)
[2026-06-08T08:57:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=134290)
[2026-06-08T08:57:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=81380)
[2026-06-08T08:57:39] Filtering fusions with <2 supporting reads (remaining=7316)
[2026-06-08T08:57:40] Filtering fusions with an e-value >=0.3 (remaining=2257)
[2026-06-08T08:57:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2270)
[2026-06-08T08:57:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2170)
[2026-06-08T08:57:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2170)
[2026-06-08T08:57:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1810)
[2026-06-08T08:57:49] Searching for fusions with spliced split reads (remaining=1934)
[2026-06-08T08:57:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=1328)
[2026-06-08T08:57:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1314)
[2026-06-08T08:57:54] Searching for fusions with >=4 spliced events (remaining=1430)
[2026-06-08T08:57:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=486)
[2026-06-08T08:58:07] Filtering fusions with anchors <=23nt (remaining=363)
[2026-06-08T08:58:08] Filtering end-to-end fusions with low support (remaining=351)
[2026-06-08T08:58:08] Filtering fusions with no coverage around the breakpoints (remaining=335)
[2026-06-08T08:58:08] Indexing gene sequences 
[2026-06-08T08:58:11] Filtering genes with >=30% identity (remaining=102)
[2026-06-08T08:58:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=32)
[2026-06-08T08:58:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=28)
[2026-06-08T08:58:13] Searching for additional isoforms (remaining=37)
[2026-06-08T08:58:14] Assigning confidence scores to events 
[2026-06-08T08:58:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:15] Writing fusions to file '659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:16] Writing discarded fusions to file '659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:31] Freeing resources
[2026-06-08T08:58:48] Done (elapsed time=00:10:40, CPU time=00:10:39, peak memory=16gb)