[2026-06-04T21:13:03] Launching Arriba 2.4.0
[2026-06-04T21:13:03] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:13:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:13:15] Reading chimeric alignments from '659_djb-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9163259)
[2026-06-04T21:19:27] Marking multi-mapping alignments (marked=5788866)
[2026-06-04T21:19:30] Detecting strandedness (no)
[2026-06-04T21:19:30] Annotating alignments 
[2026-06-04T21:20:01] Filtering duplicates (remaining=5291113)
[2026-06-04T21:20:06] 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=5027619)
[2026-06-04T21:20:08] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5027619)
[2026-06-04T21:20:09] Filtering viral contigs with expression lower than the top 5 (remaining=5027619)
[2026-06-04T21:20:13] Filtering viral contigs with less than 5% coverage (remaining=5027619)
[2026-06-04T21:20:15] Estimating fragment length (mate gap mean=-87.5046, mate gap stddev=26.9442, read length mean=127.167)
[2026-06-04T21:20:15] Filtering read-through fragments with a distance <=10000bp (remaining=4713085)
[2026-06-04T21:20:17] Filtering inconsistently clipped mates (remaining=4635369)
[2026-06-04T21:20:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4486294)
[2026-06-04T21:20:22] Filtering fragments with small insert size (remaining=4485508)
[2026-06-04T21:20:24] Filtering alignments with long gaps (remaining=4485508)
[2026-06-04T21:20:25] Filtering fragments with both mates in the same gene (remaining=4484519)
[2026-06-04T21:20:27] Filtering fusions arising from hairpin structures (remaining=4263657)
[2026-06-04T21:20:29] Filtering reads with a mismatch p-value <=0.01 (remaining=2158733)
[2026-06-04T21:20:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=934755)
[2026-06-04T21:20:47] Finding fusions and counting supporting reads (total=659597)
[2026-06-04T21:20:59] Merging adjacent fusion breakpoints (remaining=651060)
[2026-06-04T21:21:00] Filtering multi-mapping fusions by alignment score and read support (remaining=384842)
[2026-06-04T21:21:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:21:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=383383)
[2026-06-04T21:21:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=222487)
[2026-06-04T21:21:33] Filtering fusions with <2 supporting reads (remaining=29268)
[2026-06-04T21:21:33] Filtering fusions with an e-value >=0.3 (remaining=7069)
[2026-06-04T21:21:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7118)
[2026-06-04T21:21:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7024)
[2026-06-04T21:21:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7027)
[2026-06-04T21:21:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6722)
[2026-06-04T21:21:43] Searching for fusions with spliced split reads (remaining=6848)
[2026-06-04T21:21:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=4524)
[2026-06-04T21:21:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4480)
[2026-06-04T21:21:48] Searching for fusions with >=4 spliced events (remaining=5311)
[2026-06-04T21:21:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1909)
[2026-06-04T21:22:02] Filtering fusions with anchors <=23nt (remaining=1576)
[2026-06-04T21:22:02] Filtering end-to-end fusions with low support (remaining=1536)
[2026-06-04T21:22:03] Filtering fusions with no coverage around the breakpoints (remaining=1494)
[2026-06-04T21:22:03] Indexing gene sequences 
[2026-06-04T21:22:09] Filtering genes with >=30% identity (remaining=448)
[2026-06-04T21:22:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=199)
[2026-06-04T21:22:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=179)
[2026-06-04T21:22:17] Searching for additional isoforms (remaining=247)
[2026-06-04T21:22:18] Assigning confidence scores to events 
[2026-06-04T21:22:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:22:21] Writing fusions to file '659_djb-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:22:23] Writing discarded fusions to file '659_djb-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:22:42] Freeing resources
[2026-06-04T21:22:57] Done (elapsed time=00:09:54, CPU time=00:09:53, peak memory=13.7gb)