[2026-06-08T08:40:28] Launching Arriba 2.4.0
[2026-06-08T08:40:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:49] Reading chimeric alignments from '659_epP-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=11110065)
[2026-06-08T08:50:17] Marking multi-mapping alignments (marked=7187543)
[2026-06-08T08:50:24] Detecting strandedness (no)
[2026-06-08T08:50:24] Annotating alignments 
[2026-06-08T08:51:43] Filtering duplicates (remaining=3436271)
[2026-06-08T08:51:53] 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=3227582)
[2026-06-08T08:51:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3227582)
[2026-06-08T08:52:01] Filtering viral contigs with expression lower than the top 5 (remaining=3227582)
[2026-06-08T08:52:09] Filtering viral contigs with less than 5% coverage (remaining=3227582)
[2026-06-08T08:52:12] Estimating fragment length (mate gap mean=-87.8096, mate gap stddev=28.4663, read length mean=133.315)
[2026-06-08T08:52:13] Filtering read-through fragments with a distance <=10000bp (remaining=3047923)
[2026-06-08T08:52:16] Filtering inconsistently clipped mates (remaining=3001906)
[2026-06-08T08:52:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2838310)
[2026-06-08T08:52:25] Filtering fragments with small insert size (remaining=2837852)
[2026-06-08T08:52:29] Filtering alignments with long gaps (remaining=2837852)
[2026-06-08T08:52:33] Filtering fragments with both mates in the same gene (remaining=2837310)
[2026-06-08T08:52:36] Filtering fusions arising from hairpin structures (remaining=2710648)
[2026-06-08T08:52:40] Filtering reads with a mismatch p-value <=0.01 (remaining=1144755)
[2026-06-08T08:52:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=404318)
[2026-06-08T08:53:00] Finding fusions and counting supporting reads (total=348329)
[2026-06-08T08:53:22] Merging adjacent fusion breakpoints (remaining=345548)
[2026-06-08T08:53:24] Filtering multi-mapping fusions by alignment score and read support (remaining=199175)
[2026-06-08T08:54:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=197317)
[2026-06-08T08:54:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=105598)
[2026-06-08T08:54:23] Filtering fusions with <2 supporting reads (remaining=12114)
[2026-06-08T08:54:24] Filtering fusions with an e-value >=0.3 (remaining=4143)
[2026-06-08T08:54:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4166)
[2026-06-08T08:54:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4090)
[2026-06-08T08:54:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4090)
[2026-06-08T08:54:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2495)
[2026-06-08T08:54:38] Searching for fusions with spliced split reads (remaining=2543)
[2026-06-08T08:54:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=1807)
[2026-06-08T08:54:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1784)
[2026-06-08T08:54:47] Searching for fusions with >=4 spliced events (remaining=1978)
[2026-06-08T08:54:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=638)
[2026-06-08T08:55:08] Filtering fusions with anchors <=23nt (remaining=509)
[2026-06-08T08:55:08] Filtering end-to-end fusions with low support (remaining=481)
[2026-06-08T08:55:09] Filtering fusions with no coverage around the breakpoints (remaining=464)
[2026-06-08T08:55:10] Indexing gene sequences 
[2026-06-08T08:55:14] Filtering genes with >=30% identity (remaining=131)
[2026-06-08T08:55:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=46)
[2026-06-08T08:55:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=46)
[2026-06-08T08:55:18] Searching for additional isoforms (remaining=70)
[2026-06-08T08:55:19] Assigning confidence scores to events 
[2026-06-08T08:55:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:22] Writing fusions to file '659_epP-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:23] Writing discarded fusions to file '659_epP-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:51] Freeing resources
[2026-06-08T08:56:33] Done (elapsed time=00:16:05, CPU time=00:16:05, peak memory=15.6gb)