[2026-06-08T08:54:33] Launching Arriba 2.4.0
[2026-06-08T08:54:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:53] Reading chimeric alignments from '659_dES-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=12198494)
[2026-06-08T09:03:21] Marking multi-mapping alignments (marked=7577845)
[2026-06-08T09:03:27] Detecting strandedness (reverse)
[2026-06-08T09:03:27] Assigning strands to alignments 
[2026-06-08T09:03:29] Annotating alignments 
[2026-06-08T09:04:09] Filtering duplicates (remaining=7572531)
[2026-06-08T09:04:17] 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=7382100)
[2026-06-08T09:04:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7382100)
[2026-06-08T09:04:21] Filtering viral contigs with expression lower than the top 5 (remaining=7382100)
[2026-06-08T09:04:27] Filtering viral contigs with less than 5% coverage (remaining=7382100)
[2026-06-08T09:04:29] Estimating fragment length (mate gap mean=-89.9939, mate gap stddev=28.144, read length mean=136.853)
[2026-06-08T09:04:30] Filtering read-through fragments with a distance <=10000bp (remaining=6887242)
[2026-06-08T09:04:32] Filtering inconsistently clipped mates (remaining=6773222)
[2026-06-08T09:04:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6566522)
[2026-06-08T09:04:40] Filtering fragments with small insert size (remaining=6565813)
[2026-06-08T09:04:42] Filtering alignments with long gaps (remaining=6565813)
[2026-06-08T09:04:45] Filtering fragments with both mates in the same gene (remaining=6564722)
[2026-06-08T09:04:48] Filtering fusions arising from hairpin structures (remaining=6144101)
[2026-06-08T09:04:51] Filtering reads with a mismatch p-value <=0.01 (remaining=3311560)
[2026-06-08T09:05:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=1387399)
[2026-06-08T09:05:24] Finding fusions and counting supporting reads (total=1021576)
[2026-06-08T09:05:44] Merging adjacent fusion breakpoints (remaining=1010380)
[2026-06-08T09:05:46] Filtering multi-mapping fusions by alignment score and read support (remaining=586843)
[2026-06-08T09:06:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:06:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=583546)
[2026-06-08T09:06:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=330820)
[2026-06-08T09:06:36] Filtering fusions with <2 supporting reads (remaining=42498)
[2026-06-08T09:06:37] Filtering fusions with an e-value >=0.3 (remaining=10052)
[2026-06-08T09:06:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10098)
[2026-06-08T09:06:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9923)
[2026-06-08T09:06:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9958)
[2026-06-08T09:06:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8935)
[2026-06-08T09:06:50] Searching for fusions with spliced split reads (remaining=8958)
[2026-06-08T09:06:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=5498)
[2026-06-08T09:06:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5432)
[2026-06-08T09:06:59] Searching for fusions with >=4 spliced events (remaining=7227)
[2026-06-08T09:07:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3158)
[2026-06-08T09:07:18] Filtering fusions with anchors <=23nt (remaining=2770)
[2026-06-08T09:07:18] Filtering end-to-end fusions with low support (remaining=2705)
[2026-06-08T09:07:19] Filtering fusions with no coverage around the breakpoints (remaining=2649)
[2026-06-08T09:07:20] Indexing gene sequences 
[2026-06-08T09:07:30] Filtering genes with >=30% identity (remaining=814)
[2026-06-08T09:07:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=420)
[2026-06-08T09:07:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=300)
[2026-06-08T09:07:44] Searching for additional isoforms (remaining=469)
[2026-06-08T09:07:46] Assigning confidence scores to events 
[2026-06-08T09:07:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:07:50] Writing fusions to file '659_dES-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:07:54] Writing discarded fusions to file '659_dES-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:35] Freeing resources
[2026-06-08T09:08:59] Done (elapsed time=00:14:26, CPU time=00:14:25, peak memory=16.9gb)