[2026-06-04T21:13:00] Launching Arriba 2.4.0
[2026-06-04T21:13:00] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:13:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:13:12] Reading chimeric alignments from '659_cwv-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10752129)
[2026-06-04T21:19:47] Marking multi-mapping alignments (marked=6856468)
[2026-06-04T21:19:51] Detecting strandedness (reverse)
[2026-06-04T21:19:51] Assigning strands to alignments 
[2026-06-04T21:19:53] Annotating alignments 
[2026-06-04T21:20:24] Filtering duplicates (remaining=8115057)
[2026-06-04T21:20:32] 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=7460256)
[2026-06-04T21:20:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7460256)
[2026-06-04T21:20:36] Filtering viral contigs with expression lower than the top 5 (remaining=7460256)
[2026-06-04T21:20:41] Filtering viral contigs with less than 5% coverage (remaining=7460256)
[2026-06-04T21:20:43] Estimating fragment length (mate gap mean=-84.0185, mate gap stddev=30.1613, read length mean=130.977)
[2026-06-04T21:20:43] Filtering read-through fragments with a distance <=10000bp (remaining=7117571)
[2026-06-04T21:20:45] Filtering inconsistently clipped mates (remaining=7019958)
[2026-06-04T21:20:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6850900)
[2026-06-04T21:20:52] Filtering fragments with small insert size (remaining=6849852)
[2026-06-04T21:20:54] Filtering alignments with long gaps (remaining=6849851)
[2026-06-04T21:20:56] Filtering fragments with both mates in the same gene (remaining=6848728)
[2026-06-04T21:20:58] Filtering fusions arising from hairpin structures (remaining=6508166)
[2026-06-04T21:21:01] Filtering reads with a mismatch p-value <=0.01 (remaining=3525607)
[2026-06-04T21:21:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=1470759)
[2026-06-04T21:21:28] Finding fusions and counting supporting reads (total=1182749)
[2026-06-04T21:21:47] Merging adjacent fusion breakpoints (remaining=1176291)
[2026-06-04T21:21:49] Filtering multi-mapping fusions by alignment score and read support (remaining=708661)
[2026-06-04T21:22:30] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:22:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=706757)
[2026-06-04T21:22:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=512980)
[2026-06-04T21:22:42] Filtering fusions with <2 supporting reads (remaining=40441)
[2026-06-04T21:22:43] Filtering fusions with an e-value >=0.3 (remaining=11613)
[2026-06-04T21:22:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11684)
[2026-06-04T21:22:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11624)
[2026-06-04T21:22:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11631)
[2026-06-04T21:22:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6962)
[2026-06-04T21:23:01] Searching for fusions with spliced split reads (remaining=7086)
[2026-06-04T21:23:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=4105)
[2026-06-04T21:23:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4077)
[2026-06-04T21:23:11] Searching for fusions with >=4 spliced events (remaining=4904)
[2026-06-04T21:23:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1903)
[2026-06-04T21:23:28] Filtering fusions with anchors <=23nt (remaining=1253)
[2026-06-04T21:23:29] Filtering end-to-end fusions with low support (remaining=1232)
[2026-06-04T21:23:30] Filtering fusions with no coverage around the breakpoints (remaining=1209)
[2026-06-04T21:23:31] Indexing gene sequences 
[2026-06-04T21:23:36] Filtering genes with >=30% identity (remaining=360)
[2026-06-04T21:23:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=160)
[2026-06-04T21:23:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=155)
[2026-06-04T21:23:45] Searching for additional isoforms (remaining=198)
[2026-06-04T21:23:47] Assigning confidence scores to events 
[2026-06-04T21:23:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:23:52] Writing fusions to file '659_cwv-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:23:53] Writing discarded fusions to file '659_cwv-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:24:27] Freeing resources
[2026-06-04T21:24:48] Done (elapsed time=00:11:48, CPU time=00:11:47, peak memory=15.5gb)