[2026-06-08T08:30:06] Launching Arriba 2.4.0
[2026-06-08T08:30:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:21] Reading chimeric alignments from '659_cRB-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9503871)
[2026-06-08T08:35:33] Marking multi-mapping alignments (marked=6069130)
[2026-06-08T08:35:37] Detecting strandedness (reverse)
[2026-06-08T08:35:37] Assigning strands to alignments 
[2026-06-08T08:35:38] Annotating alignments 
[2026-06-08T08:36:06] Filtering duplicates (remaining=2734984)
[2026-06-08T08:36:10] 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=2573490)
[2026-06-08T08:36:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2573490)
[2026-06-08T08:36:13] Filtering viral contigs with expression lower than the top 5 (remaining=2573490)
[2026-06-08T08:36:17] Filtering viral contigs with less than 5% coverage (remaining=2573490)
[2026-06-08T08:36:19] Estimating fragment length (mate gap mean=-84.9613, mate gap stddev=27.0293, read length mean=121.701)
[2026-06-08T08:36:19] Filtering read-through fragments with a distance <=10000bp (remaining=2419009)
[2026-06-08T08:36:20] Filtering inconsistently clipped mates (remaining=2371242)
[2026-06-08T08:36:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2265395)
[2026-06-08T08:36:24] Filtering fragments with small insert size (remaining=2264699)
[2026-06-08T08:36:26] Filtering alignments with long gaps (remaining=2264698)
[2026-06-08T08:36:28] Filtering fragments with both mates in the same gene (remaining=2264231)
[2026-06-08T08:36:29] Filtering fusions arising from hairpin structures (remaining=2159024)
[2026-06-08T08:36:31] Filtering reads with a mismatch p-value <=0.01 (remaining=802409)
[2026-06-08T08:36:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=352838)
[2026-06-08T08:36:42] Finding fusions and counting supporting reads (total=317889)
[2026-06-08T08:36:53] Merging adjacent fusion breakpoints (remaining=314044)
[2026-06-08T08:36:54] Filtering multi-mapping fusions by alignment score and read support (remaining=175877)
[2026-06-08T08:37:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:37:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=175109)
[2026-06-08T08:37:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=97711)
[2026-06-08T08:37:22] Filtering fusions with <2 supporting reads (remaining=9582)
[2026-06-08T08:37:22] Filtering fusions with an e-value >=0.3 (remaining=2117)
[2026-06-08T08:37:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2146)
[2026-06-08T08:37:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2102)
[2026-06-08T08:37:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2102)
[2026-06-08T08:37:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2057)
[2026-06-08T08:37:29] Searching for fusions with spliced split reads (remaining=2154)
[2026-06-08T08:37:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=1601)
[2026-06-08T08:37:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1581)
[2026-06-08T08:37:33] Searching for fusions with >=4 spliced events (remaining=1712)
[2026-06-08T08:37:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=530)
[2026-06-08T08:37:46] Filtering fusions with anchors <=23nt (remaining=453)
[2026-06-08T08:37:46] Filtering end-to-end fusions with low support (remaining=441)
[2026-06-08T08:37:47] Filtering fusions with no coverage around the breakpoints (remaining=427)
[2026-06-08T08:37:47] Indexing gene sequences 
[2026-06-08T08:37:49] Filtering genes with >=30% identity (remaining=155)
[2026-06-08T08:37:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=52)
[2026-06-08T08:37:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=52)
[2026-06-08T08:37:51] Searching for additional isoforms (remaining=59)
[2026-06-08T08:37:52] Assigning confidence scores to events 
[2026-06-08T08:37:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:53] Writing fusions to file '659_cRB-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:37:54] Writing discarded fusions to file '659_cRB-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:08] Freeing resources
[2026-06-08T08:38:22] Done (elapsed time=00:08:16, CPU time=00:08:16, peak memory=13.9gb)