[2026-06-04T21:17:47] Launching Arriba 2.4.0
[2026-06-04T21:17:47] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:17:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:17:58] Reading chimeric alignments from '659_cVw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10000561)
[2026-06-04T21:24:49] Marking multi-mapping alignments (marked=6322924)
[2026-06-04T21:24:53] Detecting strandedness (reverse)
[2026-06-04T21:24:53] Assigning strands to alignments 
[2026-06-04T21:24:55] Annotating alignments 
[2026-06-04T21:25:26] Filtering duplicates (remaining=6887278)
[2026-06-04T21:25:32] 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=6527417)
[2026-06-04T21:25:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6527417)
[2026-06-04T21:25:37] Filtering viral contigs with expression lower than the top 5 (remaining=6527417)
[2026-06-04T21:25:42] Filtering viral contigs with less than 5% coverage (remaining=6527417)
[2026-06-04T21:25:44] Estimating fragment length (mate gap mean=-87.5011, mate gap stddev=30.6064, read length mean=137.399)
[2026-06-04T21:25:44] Filtering read-through fragments with a distance <=10000bp (remaining=6081306)
[2026-06-04T21:25:46] Filtering inconsistently clipped mates (remaining=5980167)
[2026-06-04T21:25:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5750332)
[2026-06-04T21:25:53] Filtering fragments with small insert size (remaining=5749813)
[2026-06-04T21:25:55] Filtering alignments with long gaps (remaining=5749811)
[2026-06-04T21:25:57] Filtering fragments with both mates in the same gene (remaining=5748712)
[2026-06-04T21:26:00] Filtering fusions arising from hairpin structures (remaining=5363344)
[2026-06-04T21:26:02] Filtering reads with a mismatch p-value <=0.01 (remaining=2898370)
[2026-06-04T21:26:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=1218616)
[2026-06-04T21:26:28] Finding fusions and counting supporting reads (total=858224)
[2026-06-04T21:26:43] Merging adjacent fusion breakpoints (remaining=851143)
[2026-06-04T21:26:44] Filtering multi-mapping fusions by alignment score and read support (remaining=537982)
[2026-06-04T21:27:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:27:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=534581)
[2026-06-04T21:27:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=291720)
[2026-06-04T21:27:22] Filtering fusions with <2 supporting reads (remaining=41527)
[2026-06-04T21:27:23] Filtering fusions with an e-value >=0.3 (remaining=13728)
[2026-06-04T21:27:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13786)
[2026-06-04T21:27:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13684)
[2026-06-04T21:27:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13684)
[2026-06-04T21:27:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10227)
[2026-06-04T21:27:34] Searching for fusions with spliced split reads (remaining=10250)
[2026-06-04T21:27:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=5155)
[2026-06-04T21:27:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5115)
[2026-06-04T21:27:41] Searching for fusions with >=4 spliced events (remaining=6146)
[2026-06-04T21:27:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2141)
[2026-06-04T21:27:58] Filtering fusions with anchors <=23nt (remaining=1605)
[2026-06-04T21:27:59] Filtering end-to-end fusions with low support (remaining=1568)
[2026-06-04T21:27:59] Filtering fusions with no coverage around the breakpoints (remaining=1528)
[2026-06-04T21:28:00] Indexing gene sequences 
[2026-06-04T21:28:05] Filtering genes with >=30% identity (remaining=490)
[2026-06-04T21:28:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=240)
[2026-06-04T21:28:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-04T21:28:13] Searching for additional isoforms (remaining=243)
[2026-06-04T21:28:14] Assigning confidence scores to events 
[2026-06-04T21:28:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:28:17] Writing fusions to file '659_cVw-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:28:20] Writing discarded fusions to file '659_cVw-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:28:46] Freeing resources
[2026-06-04T21:29:03] Done (elapsed time=00:11:16, CPU time=00:11:15, peak memory=14.8gb)