[2026-06-04T21:14:47] Launching Arriba 2.4.0
[2026-06-04T21:14:47] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:14:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:14:59] Reading chimeric alignments from '659_bjQ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10962838)
[2026-06-04T21:21:35] Marking multi-mapping alignments (marked=6949165)
[2026-06-04T21:21:39] Detecting strandedness (reverse)
[2026-06-04T21:21:39] Assigning strands to alignments 
[2026-06-04T21:21:41] Annotating alignments 
[2026-06-04T21:22:14] Filtering duplicates (remaining=7686832)
[2026-06-04T21:22:22] 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=7266745)
[2026-06-04T21:22:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7266745)
[2026-06-04T21:22:26] Filtering viral contigs with expression lower than the top 5 (remaining=7266745)
[2026-06-04T21:22:31] Filtering viral contigs with less than 5% coverage (remaining=7266745)
[2026-06-04T21:22:33] Estimating fragment length (mate gap mean=-85.9378, mate gap stddev=29.406, read length mean=130.379)
[2026-06-04T21:22:33] Filtering read-through fragments with a distance <=10000bp (remaining=6949019)
[2026-06-04T21:22:36] Filtering inconsistently clipped mates (remaining=6820957)
[2026-06-04T21:22:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6665646)
[2026-06-04T21:22:42] Filtering fragments with small insert size (remaining=6664320)
[2026-06-04T21:22:44] Filtering alignments with long gaps (remaining=6664320)
[2026-06-04T21:22:47] Filtering fragments with both mates in the same gene (remaining=6663213)
[2026-06-04T21:22:49] Filtering fusions arising from hairpin structures (remaining=6231821)
[2026-06-04T21:22:52] Filtering reads with a mismatch p-value <=0.01 (remaining=3224550)
[2026-06-04T21:23:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=1206826)
[2026-06-04T21:23:19] Finding fusions and counting supporting reads (total=900035)
[2026-06-04T21:23:35] Merging adjacent fusion breakpoints (remaining=892351)
[2026-06-04T21:23:37] Filtering multi-mapping fusions by alignment score and read support (remaining=566774)
[2026-06-04T21:24:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:24:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=564869)
[2026-06-04T21:24:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=364781)
[2026-06-04T21:24:22] Filtering fusions with <2 supporting reads (remaining=33294)
[2026-06-04T21:24:23] Filtering fusions with an e-value >=0.3 (remaining=8130)
[2026-06-04T21:24:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8202)
[2026-06-04T21:24:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8081)
[2026-06-04T21:24:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8084)
[2026-06-04T21:24:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6634)
[2026-06-04T21:24:36] Searching for fusions with spliced split reads (remaining=6669)
[2026-06-04T21:24:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=4123)
[2026-06-04T21:24:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4073)
[2026-06-04T21:24:44] Searching for fusions with >=4 spliced events (remaining=4873)
[2026-06-04T21:24:45] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1965)
[2026-06-04T21:25:00] Filtering fusions with anchors <=23nt (remaining=1437)
[2026-06-04T21:25:01] Filtering end-to-end fusions with low support (remaining=1413)
[2026-06-04T21:25:02] Filtering fusions with no coverage around the breakpoints (remaining=1377)
[2026-06-04T21:25:02] Indexing gene sequences 
[2026-06-04T21:25:09] Filtering genes with >=30% identity (remaining=449)
[2026-06-04T21:25:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=218)
[2026-06-04T21:25:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=184)
[2026-06-04T21:25:18] Searching for additional isoforms (remaining=247)
[2026-06-04T21:25:20] Assigning confidence scores to events 
[2026-06-04T21:25:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:25:23] Writing fusions to file '659_bjQ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:25:26] Writing discarded fusions to file '659_bjQ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:25:55] Freeing resources
[2026-06-04T21:26:13] Done (elapsed time=00:11:26, CPU time=00:11:25, peak memory=15.5gb)