[2026-06-04T21:15:51] Launching Arriba 2.4.0
[2026-06-04T21:15:51] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:15:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:16:02] Reading chimeric alignments from '659_cWx-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11152997)
[2026-06-04T21:22:54] Marking multi-mapping alignments (marked=7040832)
[2026-06-04T21:22:59] Detecting strandedness (reverse)
[2026-06-04T21:22:59] Assigning strands to alignments 
[2026-06-04T21:23:01] Annotating alignments 
[2026-06-04T21:23:35] Filtering duplicates (remaining=6540191)
[2026-06-04T21:23:42] 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=6109758)
[2026-06-04T21:23:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6109758)
[2026-06-04T21:23:47] Filtering viral contigs with expression lower than the top 5 (remaining=6109758)
[2026-06-04T21:23:52] Filtering viral contigs with less than 5% coverage (remaining=6109758)
[2026-06-04T21:23:54] Estimating fragment length (mate gap mean=-87.1889, mate gap stddev=28.9735, read length mean=133.095)
[2026-06-04T21:23:54] Filtering read-through fragments with a distance <=10000bp (remaining=5666488)
[2026-06-04T21:23:57] Filtering inconsistently clipped mates (remaining=5552257)
[2026-06-04T21:23:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5367076)
[2026-06-04T21:24:03] Filtering fragments with small insert size (remaining=5366065)
[2026-06-04T21:24:05] Filtering alignments with long gaps (remaining=5366065)
[2026-06-04T21:24:07] Filtering fragments with both mates in the same gene (remaining=5364983)
[2026-06-04T21:24:10] Filtering fusions arising from hairpin structures (remaining=4978542)
[2026-06-04T21:24:13] Filtering reads with a mismatch p-value <=0.01 (remaining=2609781)
[2026-06-04T21:24:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=1101605)
[2026-06-04T21:24:36] Finding fusions and counting supporting reads (total=824588)
[2026-06-04T21:24:52] Merging adjacent fusion breakpoints (remaining=816061)
[2026-06-04T21:24:53] Filtering multi-mapping fusions by alignment score and read support (remaining=499765)
[2026-06-04T21:25:25] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:25:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=496376)
[2026-06-04T21:25:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=269989)
[2026-06-04T21:25:33] Filtering fusions with <2 supporting reads (remaining=34765)
[2026-06-04T21:25:34] Filtering fusions with an e-value >=0.3 (remaining=9430)
[2026-06-04T21:25:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9517)
[2026-06-04T21:25:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9419)
[2026-06-04T21:25:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9420)
[2026-06-04T21:25:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7906)
[2026-06-04T21:25:46] Searching for fusions with spliced split reads (remaining=8013)
[2026-06-04T21:25:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=4836)
[2026-06-04T21:25:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4793)
[2026-06-04T21:25:53] Searching for fusions with >=4 spliced events (remaining=5620)
[2026-06-04T21:25:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2033)
[2026-06-04T21:26:10] Filtering fusions with anchors <=23nt (remaining=1548)
[2026-06-04T21:26:11] Filtering end-to-end fusions with low support (remaining=1494)
[2026-06-04T21:26:12] Filtering fusions with no coverage around the breakpoints (remaining=1464)
[2026-06-04T21:26:12] Indexing gene sequences 
[2026-06-04T21:26:18] Filtering genes with >=30% identity (remaining=482)
[2026-06-04T21:26:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=212)
[2026-06-04T21:26:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=187)
[2026-06-04T21:26:24] Searching for additional isoforms (remaining=243)
[2026-06-04T21:26:25] Assigning confidence scores to events 
[2026-06-04T21:26:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:26:29] Writing fusions to file '659_cWx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:26:30] Writing discarded fusions to file '659_cWx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:26:56] Freeing resources
[2026-06-04T21:27:13] Done (elapsed time=00:11:22, CPU time=00:11:21, peak memory=15.9gb)