[2026-06-08T07:55:35] Launching Arriba 2.4.0
[2026-06-08T07:55:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:55:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:55:59] Reading chimeric alignments from '659_yV_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam' (total=4890980)
[2026-06-08T08:00:13] Marking multi-mapping alignments (marked=3258370)
[2026-06-08T08:00:15] Detecting strandedness (reverse)
[2026-06-08T08:00:15] Assigning strands to alignments 
[2026-06-08T08:00:16] Annotating alignments 
[2026-06-08T08:00:36] Filtering duplicates (remaining=2827383)
[2026-06-08T08:00:41] 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=2616670)
[2026-06-08T08:00:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2616670)
[2026-06-08T08:00:43] Filtering viral contigs with expression lower than the top 5 (remaining=2616670)
[2026-06-08T08:00:45] Filtering viral contigs with less than 5% coverage (remaining=2616670)
[2026-06-08T08:00:46] Estimating fragment length (mate gap mean=-89.2673, mate gap stddev=27.5096, read length mean=126.81)
[2026-06-08T08:00:46] Filtering read-through fragments with a distance <=10000bp (remaining=2400963)
[2026-06-08T08:00:47] Filtering inconsistently clipped mates (remaining=2331505)
[2026-06-08T08:00:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2180919)
[2026-06-08T08:00:51] Filtering fragments with small insert size (remaining=2180219)
[2026-06-08T08:00:52] Filtering alignments with long gaps (remaining=2180218)
[2026-06-08T08:00:53] Filtering fragments with both mates in the same gene (remaining=2179701)
[2026-06-08T08:00:54] Filtering fusions arising from hairpin structures (remaining=1969846)
[2026-06-08T08:00:56] Filtering reads with a mismatch p-value <=0.01 (remaining=745839)
[2026-06-08T08:01:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=534535)
[2026-06-08T08:01:09] Finding fusions and counting supporting reads (total=462325)
[2026-06-08T08:01:18] Merging adjacent fusion breakpoints (remaining=459666)
[2026-06-08T08:01:19] Filtering multi-mapping fusions by alignment score and read support (remaining=263300)
[2026-06-08T08:01:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:01:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=262378)
[2026-06-08T08:01:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=154592)
[2026-06-08T08:01:42] Filtering fusions with <2 supporting reads (remaining=13323)
[2026-06-08T08:01:43] Filtering fusions with an e-value >=0.3 (remaining=2962)
[2026-06-08T08:01:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3025)
[2026-06-08T08:01:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2970)
[2026-06-08T08:01:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2970)
[2026-06-08T08:01:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2803)
[2026-06-08T08:01:49] Searching for fusions with spliced split reads (remaining=2850)
[2026-06-08T08:01:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=2165)
[2026-06-08T08:01:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2141)
[2026-06-08T08:01:53] Searching for fusions with >=4 spliced events (remaining=2389)
[2026-06-08T08:01:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=946)
[2026-06-08T08:02:10] Filtering fusions with anchors <=23nt (remaining=785)
[2026-06-08T08:02:10] Filtering end-to-end fusions with low support (remaining=766)
[2026-06-08T08:02:10] Filtering fusions with no coverage around the breakpoints (remaining=743)
[2026-06-08T08:02:11] Indexing gene sequences 
[2026-06-08T08:02:14] Filtering genes with >=30% identity (remaining=272)
[2026-06-08T08:02:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=143)
[2026-06-08T08:02:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=137)
[2026-06-08T08:02:18] Searching for additional isoforms (remaining=157)
[2026-06-08T08:02:18] Assigning confidence scores to events 
[2026-06-08T08:02:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:02:20] Writing fusions to file '659_yV_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:02:21] Writing discarded fusions to file '659_yV_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:02:40] Freeing resources
[2026-06-08T08:02:49] Done (elapsed time=00:07:14, CPU time=00:07:13, peak memory=9.56gb)