[2026-06-04T21:09:42] Launching Arriba 2.4.0
[2026-06-04T21:09:42] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:09:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:09:53] Reading chimeric alignments from '659_dXa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12542044)
[2026-06-04T21:16:13] Marking multi-mapping alignments (marked=8209787)
[2026-06-04T21:16:17] Detecting strandedness (reverse)
[2026-06-04T21:16:17] Assigning strands to alignments 
[2026-06-04T21:16:20] Annotating alignments 
[2026-06-04T21:16:54] Filtering duplicates (remaining=3606560)
[2026-06-04T21:16:59] 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=3284382)
[2026-06-04T21:17:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3284382)
[2026-06-04T21:17:03] Filtering viral contigs with expression lower than the top 5 (remaining=3284382)
[2026-06-04T21:17:08] Filtering viral contigs with less than 5% coverage (remaining=3284382)
[2026-06-04T21:17:11] Estimating fragment length (mate gap mean=-82.5796, mate gap stddev=28.6889, read length mean=126.61)
[2026-06-04T21:17:11] Filtering read-through fragments with a distance <=10000bp (remaining=3160780)
[2026-06-04T21:17:13] Filtering inconsistently clipped mates (remaining=3108686)
[2026-06-04T21:17:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2992070)
[2026-06-04T21:17:19] Filtering fragments with small insert size (remaining=2991303)
[2026-06-04T21:17:21] Filtering alignments with long gaps (remaining=2991303)
[2026-06-04T21:17:23] Filtering fragments with both mates in the same gene (remaining=2990570)
[2026-06-04T21:17:26] Filtering fusions arising from hairpin structures (remaining=2862242)
[2026-06-04T21:17:28] Filtering reads with a mismatch p-value <=0.01 (remaining=1277755)
[2026-06-04T21:17:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=323293)
[2026-06-04T21:17:45] Finding fusions and counting supporting reads (total=269764)
[2026-06-04T21:18:06] Merging adjacent fusion breakpoints (remaining=268342)
[2026-06-04T21:18:07] Filtering multi-mapping fusions by alignment score and read support (remaining=151375)
[2026-06-04T21:18:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:18:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=149487)
[2026-06-04T21:18:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=83239)
[2026-06-04T21:18:47] Filtering fusions with <2 supporting reads (remaining=7908)
[2026-06-04T21:18:47] Filtering fusions with an e-value >=0.3 (remaining=2539)
[2026-06-04T21:18:47] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2571)
[2026-06-04T21:18:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2493)
[2026-06-04T21:18:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2496)
[2026-06-04T21:18:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1877)
[2026-06-04T21:18:57] Searching for fusions with spliced split reads (remaining=1919)
[2026-06-04T21:19:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=1402)
[2026-06-04T21:19:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1376)
[2026-06-04T21:19:02] Searching for fusions with >=4 spliced events (remaining=1506)
[2026-06-04T21:19:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=543)
[2026-06-04T21:19:15] Filtering fusions with anchors <=23nt (remaining=435)
[2026-06-04T21:19:15] Filtering end-to-end fusions with low support (remaining=429)
[2026-06-04T21:19:15] Filtering fusions with no coverage around the breakpoints (remaining=420)
[2026-06-04T21:19:16] Indexing gene sequences 
[2026-06-04T21:19:18] Filtering genes with >=30% identity (remaining=196)
[2026-06-04T21:19:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=127)
[2026-06-04T21:19:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-04T21:19:22] Searching for additional isoforms (remaining=141)
[2026-06-04T21:19:23] Assigning confidence scores to events 
[2026-06-04T21:19:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:19:25] Writing fusions to file '659_dXa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:19:26] Writing discarded fusions to file '659_dXa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:19:40] Freeing resources
[2026-06-04T21:20:02] Done (elapsed time=00:10:20, CPU time=00:10:19, peak memory=16.5gb)