[2026-06-08T08:38:20] Launching Arriba 2.4.0
[2026-06-08T08:38:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:33] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:38] Reading chimeric alignments from '659_dES-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10337255)
[2026-06-08T08:47:32] Marking multi-mapping alignments (marked=6639027)
[2026-06-08T08:47:39] Detecting strandedness (no)
[2026-06-08T08:47:39] Annotating alignments 
[2026-06-08T08:48:45] Filtering duplicates (remaining=3817409)
[2026-06-08T08:48:53] 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=3653944)
[2026-06-08T08:48:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3653944)
[2026-06-08T08:49:00] Filtering viral contigs with expression lower than the top 5 (remaining=3653944)
[2026-06-08T08:49:07] Filtering viral contigs with less than 5% coverage (remaining=3653944)
[2026-06-08T08:49:11] Estimating fragment length (mate gap mean=-88.2637, mate gap stddev=27.9533, read length mean=132.635)
[2026-06-08T08:49:11] Filtering read-through fragments with a distance <=10000bp (remaining=3436375)
[2026-06-08T08:49:15] Filtering inconsistently clipped mates (remaining=3376594)
[2026-06-08T08:49:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3233559)
[2026-06-08T08:49:24] Filtering fragments with small insert size (remaining=3233040)
[2026-06-08T08:49:27] Filtering alignments with long gaps (remaining=3233040)
[2026-06-08T08:49:31] Filtering fragments with both mates in the same gene (remaining=3232364)
[2026-06-08T08:49:34] Filtering fusions arising from hairpin structures (remaining=3056755)
[2026-06-08T08:49:38] Filtering reads with a mismatch p-value <=0.01 (remaining=1332329)
[2026-06-08T08:49:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=609231)
[2026-06-08T08:50:01] Finding fusions and counting supporting reads (total=489057)
[2026-06-08T08:50:30] Merging adjacent fusion breakpoints (remaining=483870)
[2026-06-08T08:50:32] Filtering multi-mapping fusions by alignment score and read support (remaining=267801)
[2026-06-08T08:51:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=265536)
[2026-06-08T08:51:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=146212)
[2026-06-08T08:51:45] Filtering fusions with <2 supporting reads (remaining=17584)
[2026-06-08T08:51:45] Filtering fusions with an e-value >=0.3 (remaining=4725)
[2026-06-08T08:51:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4748)
[2026-06-08T08:51:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4620)
[2026-06-08T08:51:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4628)
[2026-06-08T08:51:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4237)
[2026-06-08T08:52:00] Searching for fusions with spliced split reads (remaining=4348)
[2026-06-08T08:52:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=3017)
[2026-06-08T08:52:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2981)
[2026-06-08T08:52:09] Searching for fusions with >=4 spliced events (remaining=3583)
[2026-06-08T08:52:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1346)
[2026-06-08T08:52:28] Filtering fusions with anchors <=23nt (remaining=1134)
[2026-06-08T08:52:29] Filtering end-to-end fusions with low support (remaining=1098)
[2026-06-08T08:52:29] Filtering fusions with no coverage around the breakpoints (remaining=1073)
[2026-06-08T08:52:30] Indexing gene sequences 
[2026-06-08T08:52:37] Filtering genes with >=30% identity (remaining=325)
[2026-06-08T08:52:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=162)
[2026-06-08T08:52:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=134)
[2026-06-08T08:52:44] Searching for additional isoforms (remaining=192)
[2026-06-08T08:52:46] Assigning confidence scores to events 
[2026-06-08T08:52:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:49] Writing fusions to file '659_dES-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:51] Writing discarded fusions to file '659_dES-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:23] Freeing resources
[2026-06-08T08:53:53] Done (elapsed time=00:15:33, CPU time=00:15:31, peak memory=14.9gb)