[2026-06-04T21:12:45] Launching Arriba 2.4.0
[2026-06-04T21:12:45] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:12:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:12:56] Reading chimeric alignments from '659_bKP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11860002)
[2026-06-04T21:19:34] Marking multi-mapping alignments (marked=7835323)
[2026-06-04T21:19:39] Detecting strandedness (reverse)
[2026-06-04T21:19:39] Assigning strands to alignments 
[2026-06-04T21:19:41] Annotating alignments 
[2026-06-04T21:20:18] Filtering duplicates (remaining=6275851)
[2026-06-04T21:20:26] 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=5919930)
[2026-06-04T21:20:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5919930)
[2026-06-04T21:20:30] Filtering viral contigs with expression lower than the top 5 (remaining=5919930)
[2026-06-04T21:20:36] Filtering viral contigs with less than 5% coverage (remaining=5919930)
[2026-06-04T21:20:38] Estimating fragment length (mate gap mean=-88.8743, mate gap stddev=28.0032, read length mean=127.739)
[2026-06-04T21:20:38] Filtering read-through fragments with a distance <=10000bp (remaining=5492646)
[2026-06-04T21:20:41] Filtering inconsistently clipped mates (remaining=5385712)
[2026-06-04T21:20:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5179348)
[2026-06-04T21:20:47] Filtering fragments with small insert size (remaining=5178346)
[2026-06-04T21:20:50] Filtering alignments with long gaps (remaining=5178346)
[2026-06-04T21:20:52] Filtering fragments with both mates in the same gene (remaining=5177497)
[2026-06-04T21:20:55] Filtering fusions arising from hairpin structures (remaining=4841182)
[2026-06-04T21:20:57] Filtering reads with a mismatch p-value <=0.01 (remaining=2259108)
[2026-06-04T21:21:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=985749)
[2026-06-04T21:21:21] Finding fusions and counting supporting reads (total=771534)
[2026-06-04T21:21:38] Merging adjacent fusion breakpoints (remaining=758972)
[2026-06-04T21:21:40] Filtering multi-mapping fusions by alignment score and read support (remaining=452839)
[2026-06-04T21:22:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:22:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=451437)
[2026-06-04T21:22:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=243272)
[2026-06-04T21:22:24] Filtering fusions with <2 supporting reads (remaining=29409)
[2026-06-04T21:22:24] Filtering fusions with an e-value >=0.3 (remaining=6736)
[2026-06-04T21:22:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6778)
[2026-06-04T21:22:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6639)
[2026-06-04T21:22:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6642)
[2026-06-04T21:22:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6461)
[2026-06-04T21:22:37] Searching for fusions with spliced split reads (remaining=6555)
[2026-06-04T21:22:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=4544)
[2026-06-04T21:22:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4494)
[2026-06-04T21:22:44] Searching for fusions with >=4 spliced events (remaining=5271)
[2026-06-04T21:22:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2194)
[2026-06-04T21:23:03] Filtering fusions with anchors <=23nt (remaining=1596)
[2026-06-04T21:23:04] Filtering end-to-end fusions with low support (remaining=1548)
[2026-06-04T21:23:05] Filtering fusions with no coverage around the breakpoints (remaining=1503)
[2026-06-04T21:23:06] Indexing gene sequences 
[2026-06-04T21:23:11] Filtering genes with >=30% identity (remaining=417)
[2026-06-04T21:23:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=83)
[2026-06-04T21:23:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=82)
[2026-06-04T21:23:16] Searching for additional isoforms (remaining=113)
[2026-06-04T21:23:18] Assigning confidence scores to events 
[2026-06-04T21:23:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:23:21] Writing fusions to file '659_bKP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:23:23] Writing discarded fusions to file '659_bKP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:23:48] Freeing resources
[2026-06-04T21:24:07] Done (elapsed time=00:11:22, CPU time=00:11:21, peak memory=16.7gb)