[2026-06-08T08:28:41] Launching Arriba 2.4.0
[2026-06-08T08:28:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:55] Reading chimeric alignments from '659_dXa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12542044)
[2026-06-08T08:36:57] Marking multi-mapping alignments (marked=8209787)
[2026-06-08T08:37:04] Detecting strandedness (reverse)
[2026-06-08T08:37:04] Assigning strands to alignments 
[2026-06-08T08:37:08] Annotating alignments 
[2026-06-08T08:38:09] Filtering duplicates (remaining=3606560)
[2026-06-08T08:38:18] 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)
[2026-06-08T08:38:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3284382)
[2026-06-08T08:38:26] Filtering viral contigs with expression lower than the top 5 (remaining=3284382)
[2026-06-08T08:38:34] Filtering viral contigs with less than 5% coverage (remaining=3284382)
[2026-06-08T08:38:38] Estimating fragment length (mate gap mean=-82.5796, mate gap stddev=28.6889, read length mean=126.61)
[2026-06-08T08:38:38] Filtering read-through fragments with a distance <=10000bp (remaining=3160780)
[2026-06-08T08:38:42] Filtering inconsistently clipped mates (remaining=3108686)
[2026-06-08T08:38:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2992070)
[2026-06-08T08:38:51] Filtering fragments with small insert size (remaining=2991303)
[2026-06-08T08:38:55] Filtering alignments with long gaps (remaining=2991303)
[2026-06-08T08:38:58] Filtering fragments with both mates in the same gene (remaining=2990570)
[2026-06-08T08:39:02] Filtering fusions arising from hairpin structures (remaining=2862242)
[2026-06-08T08:39:06] Filtering reads with a mismatch p-value <=0.01 (remaining=1277755)
[2026-06-08T08:39:17] Filtering reads with low entropy (k-mer content >=60%) (remaining=323293)
[2026-06-08T08:39:28] Finding fusions and counting supporting reads (total=269764)
[2026-06-08T08:39:51] Merging adjacent fusion breakpoints (remaining=268342)
[2026-06-08T08:39:52] Filtering multi-mapping fusions by alignment score and read support (remaining=151375)
[2026-06-08T08:40:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=149487)
[2026-06-08T08:40:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=83239)
[2026-06-08T08:40:51] Filtering fusions with <2 supporting reads (remaining=7908)
[2026-06-08T08:40:52] Filtering fusions with an e-value >=0.3 (remaining=2539)
[2026-06-08T08:40:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2571)
[2026-06-08T08:40:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2493)
[2026-06-08T08:40:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2496)
[2026-06-08T08:40:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1877)
[2026-06-08T08:41:05] Searching for fusions with spliced split reads (remaining=1919)
[2026-06-08T08:41:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=1402)
[2026-06-08T08:41:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1376)
[2026-06-08T08:41:13] Searching for fusions with >=4 spliced events (remaining=1506)
[2026-06-08T08:41:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=543)
[2026-06-08T08:41:30] Filtering fusions with anchors <=23nt (remaining=435)
[2026-06-08T08:41:31] Filtering end-to-end fusions with low support (remaining=429)
[2026-06-08T08:41:31] Filtering fusions with no coverage around the breakpoints (remaining=420)
[2026-06-08T08:41:32] Indexing gene sequences 
[2026-06-08T08:41:36] Filtering genes with >=30% identity (remaining=196)
[2026-06-08T08:41:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=127)
[2026-06-08T08:41:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-08T08:41:42] Searching for additional isoforms (remaining=141)
[2026-06-08T08:41:43] Assigning confidence scores to events 
[2026-06-08T08:41:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:45] Writing fusions to file '659_dXa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:47] Writing discarded fusions to file '659_dXa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:14] Freeing resources
[2026-06-08T08:42:42] Done (elapsed time=00:14:01, CPU time=00:14:00, peak memory=16.5gb)