[2026-05-28T00:04:01] Launching Arriba 2.4.0
[2026-05-28T00:04:01] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:04:11] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:16] Reading chimeric alignments from '659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=2870120)
[2026-05-28T00:06:59] Marking multi-mapping alignments (marked=1742988)
[2026-05-28T00:07:01] Detecting strandedness (reverse)
[2026-05-28T00:07:01] Assigning strands to alignments 
[2026-05-28T00:07:01] Annotating alignments 
[2026-05-28T00:07:14] Filtering duplicates (remaining=1679612)
[2026-05-28T00:07:17] 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=1600400)
[2026-05-28T00:07:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1600400)
[2026-05-28T00:07:19] Filtering viral contigs with expression lower than the top 5 (remaining=1600400)
[2026-05-28T00:07:20] Filtering viral contigs with less than 5% coverage (remaining=1600400)
[2026-05-28T00:07:21] Estimating fragment length (mate gap mean=-86.9387, mate gap stddev=30.0173, read length mean=135.895)
[2026-05-28T00:07:21] Filtering read-through fragments with a distance <=10000bp (remaining=1498294)
[2026-05-28T00:07:22] Filtering inconsistently clipped mates (remaining=1469184)
[2026-05-28T00:07:23] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1428088)
[2026-05-28T00:07:24] Filtering fragments with small insert size (remaining=1427866)
[2026-05-28T00:07:25] Filtering alignments with long gaps (remaining=1427866)
[2026-05-28T00:07:25] Filtering fragments with both mates in the same gene (remaining=1427572)
[2026-05-28T00:07:26] Filtering fusions arising from hairpin structures (remaining=1326151)
[2026-05-28T00:07:27] Filtering reads with a mismatch p-value <=0.01 (remaining=590513)
[2026-05-28T00:07:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=244744)
[2026-05-28T00:07:34] Finding fusions and counting supporting reads (total=194130)
[2026-05-28T00:07:40] Merging adjacent fusion breakpoints (remaining=192459)
[2026-05-28T00:07:41] Filtering multi-mapping fusions by alignment score and read support (remaining=130675)
[2026-05-28T00:07:54] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=129597)
[2026-05-28T00:07:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=65311)
[2026-05-28T00:07:57] Filtering fusions with <2 supporting reads (remaining=10329)
[2026-05-28T00:07:58] Filtering fusions with an e-value >=0.3 (remaining=3644)
[2026-05-28T00:07:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3678)
[2026-05-28T00:07:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3656)
[2026-05-28T00:08:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3656)
[2026-05-28T00:08:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2217)
[2026-05-28T00:08:02] Searching for fusions with spliced split reads (remaining=2347)
[2026-05-28T00:08:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=1686)
[2026-05-28T00:08:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1669)
[2026-05-28T00:08:05] Searching for fusions with >=4 spliced events (remaining=1781)
[2026-05-28T00:08:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=399)
[2026-05-28T00:08:20] Filtering fusions with anchors <=23nt (remaining=317)
[2026-05-28T00:08:20] Filtering end-to-end fusions with low support (remaining=308)
[2026-05-28T00:08:20] Filtering fusions with no coverage around the breakpoints (remaining=295)
[2026-05-28T00:08:20] Indexing gene sequences 
[2026-05-28T00:08:23] Filtering genes with >=30% identity (remaining=133)
[2026-05-28T00:08:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=93)
[2026-05-28T00:08:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=86)
[2026-05-28T00:08:25] Searching for additional isoforms (remaining=102)
[2026-05-28T00:08:25] Assigning confidence scores to events 
[2026-05-28T00:08:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:26] Writing fusions to file '659_bhK-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:08:27] Writing discarded fusions to file '659_bhK-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:36] Freeing resources
[2026-05-28T00:08:43] Done (elapsed time=00:04:42, CPU time=00:04:40, peak memory=7.12gb)