[2026-06-08T08:35:49] Launching Arriba 2.4.0
[2026-06-08T08:35:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:02] Reading chimeric alignments from '659_bjQ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10962838)
[2026-06-08T08:42:51] Marking multi-mapping alignments (marked=6949165)
[2026-06-08T08:42:55] Detecting strandedness (reverse)
[2026-06-08T08:42:55] Assigning strands to alignments 
[2026-06-08T08:42:57] Annotating alignments 
[2026-06-08T08:43:32] Filtering duplicates (remaining=7686832)
[2026-06-08T08:43:40] 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)
[2026-06-08T08:43:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7266745)
[2026-06-08T08:43:44] Filtering viral contigs with expression lower than the top 5 (remaining=7266745)
[2026-06-08T08:43:49] Filtering viral contigs with less than 5% coverage (remaining=7266745)
[2026-06-08T08:43:52] Estimating fragment length (mate gap mean=-85.9378, mate gap stddev=29.406, read length mean=130.379)
[2026-06-08T08:43:52] Filtering read-through fragments with a distance <=10000bp (remaining=6949019)
[2026-06-08T08:43:54] Filtering inconsistently clipped mates (remaining=6820957)
[2026-06-08T08:43:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6665646)
[2026-06-08T08:44:01] Filtering fragments with small insert size (remaining=6664320)
[2026-06-08T08:44:03] Filtering alignments with long gaps (remaining=6664320)
[2026-06-08T08:44:05] Filtering fragments with both mates in the same gene (remaining=6663213)
[2026-06-08T08:44:08] Filtering fusions arising from hairpin structures (remaining=6231821)
[2026-06-08T08:44:10] Filtering reads with a mismatch p-value <=0.01 (remaining=3224550)
[2026-06-08T08:44:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=1206826)
[2026-06-08T08:44:38] Finding fusions and counting supporting reads (total=900035)
[2026-06-08T08:44:56] Merging adjacent fusion breakpoints (remaining=892351)
[2026-06-08T08:44:58] Filtering multi-mapping fusions by alignment score and read support (remaining=566774)
[2026-06-08T08:45:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=564869)
[2026-06-08T08:45:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=364781)
[2026-06-08T08:45:41] Filtering fusions with <2 supporting reads (remaining=33294)
[2026-06-08T08:45:42] Filtering fusions with an e-value >=0.3 (remaining=8130)
[2026-06-08T08:45:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8202)
[2026-06-08T08:45:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8081)
[2026-06-08T08:45:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8084)
[2026-06-08T08:45:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6634)
[2026-06-08T08:45:55] Searching for fusions with spliced split reads (remaining=6669)
[2026-06-08T08:46:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=4123)
[2026-06-08T08:46:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4073)
[2026-06-08T08:46:03] Searching for fusions with >=4 spliced events (remaining=4873)
[2026-06-08T08:46:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1965)
[2026-06-08T08:46:19] Filtering fusions with anchors <=23nt (remaining=1437)
[2026-06-08T08:46:20] Filtering end-to-end fusions with low support (remaining=1413)
[2026-06-08T08:46:20] Filtering fusions with no coverage around the breakpoints (remaining=1377)
[2026-06-08T08:46:21] Indexing gene sequences 
[2026-06-08T08:46:27] Filtering genes with >=30% identity (remaining=449)
[2026-06-08T08:46:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=218)
[2026-06-08T08:46:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=184)
[2026-06-08T08:46:37] Searching for additional isoforms (remaining=247)
[2026-06-08T08:46:38] Assigning confidence scores to events 
[2026-06-08T08:46:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:42] Writing fusions to file '659_bjQ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:46:44] Writing discarded fusions to file '659_bjQ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:16] Freeing resources
[2026-06-08T08:47:34] Done (elapsed time=00:11:45, CPU time=00:11:43, peak memory=15.5gb)