[2026-06-08T08:03:21] Launching Arriba 2.4.0
[2026-06-08T08:03:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:03:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:03:43] Reading chimeric alignments from '659_dcz-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=7738391)
[2026-06-08T08:08:28] Marking multi-mapping alignments (marked=5437236)
[2026-06-08T08:08:31] Detecting strandedness (reverse)
[2026-06-08T08:08:31] Assigning strands to alignments 
[2026-06-08T08:08:33] Annotating alignments 
[2026-06-08T08:08:58] Filtering duplicates (remaining=2280041)
[2026-06-08T08:09:01] 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=2100511)
[2026-06-08T08:09:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2100511)
[2026-06-08T08:09:04] Filtering viral contigs with expression lower than the top 5 (remaining=2100511)
[2026-06-08T08:09:06] Filtering viral contigs with less than 5% coverage (remaining=2100511)
[2026-06-08T08:09:08] Estimating fragment length (mate gap mean=-81.6464, mate gap stddev=26.7723, read length mean=116.185)
[2026-06-08T08:09:08] Filtering read-through fragments with a distance <=10000bp (remaining=2031950)
[2026-06-08T08:09:10] Filtering inconsistently clipped mates (remaining=1976481)
[2026-06-08T08:09:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1855529)
[2026-06-08T08:09:13] Filtering fragments with small insert size (remaining=1854489)
[2026-06-08T08:09:15] Filtering alignments with long gaps (remaining=1854489)
[2026-06-08T08:09:16] Filtering fragments with both mates in the same gene (remaining=1853891)
[2026-06-08T08:09:18] Filtering fusions arising from hairpin structures (remaining=1738264)
[2026-06-08T08:09:19] Filtering reads with a mismatch p-value <=0.01 (remaining=634861)
[2026-06-08T08:09:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=234178)
[2026-06-08T08:09:29] Finding fusions and counting supporting reads (total=208433)
[2026-06-08T08:09:38] Merging adjacent fusion breakpoints (remaining=206846)
[2026-06-08T08:09:39] Filtering multi-mapping fusions by alignment score and read support (remaining=104344)
[2026-06-08T08:10:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:10:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=103673)
[2026-06-08T08:10:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=68598)
[2026-06-08T08:10:05] Filtering fusions with <2 supporting reads (remaining=5018)
[2026-06-08T08:10:05] Filtering fusions with an e-value >=0.3 (remaining=1275)
[2026-06-08T08:10:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1311)
[2026-06-08T08:10:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1262)
[2026-06-08T08:10:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1266)
[2026-06-08T08:10:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1260)
[2026-06-08T08:10:11] Searching for fusions with spliced split reads (remaining=1342)
[2026-06-08T08:10:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=1062)
[2026-06-08T08:10:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1039)
[2026-06-08T08:10:15] Searching for fusions with >=4 spliced events (remaining=1077)
[2026-06-08T08:10:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=379)
[2026-06-08T08:10:29] Filtering fusions with anchors <=23nt (remaining=324)
[2026-06-08T08:10:29] Filtering end-to-end fusions with low support (remaining=291)
[2026-06-08T08:10:30] Filtering fusions with no coverage around the breakpoints (remaining=283)
[2026-06-08T08:10:30] Indexing gene sequences 
[2026-06-08T08:10:32] Filtering genes with >=30% identity (remaining=138)
[2026-06-08T08:10:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=83)
[2026-06-08T08:10:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=83)
[2026-06-08T08:10:34] Searching for additional isoforms (remaining=94)
[2026-06-08T08:10:34] Assigning confidence scores to events 
[2026-06-08T08:10:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:10:36] Writing fusions to file '659_dcz-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:10:37] Writing discarded fusions to file '659_dcz-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:10:49] Freeing resources
[2026-06-08T08:11:01] Done (elapsed time=00:07:40, CPU time=00:07:40, peak memory=12gb)