[2026-06-08T08:54:35] Launching Arriba 2.4.0
[2026-06-08T08:54:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:48] Reading chimeric alignments from '659_bNS-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11634836)
[2026-06-08T09:01:52] Marking multi-mapping alignments (marked=6989696)
[2026-06-08T09:01:57] Detecting strandedness (reverse)
[2026-06-08T09:01:57] Assigning strands to alignments 
[2026-06-08T09:02:00] Annotating alignments 
[2026-06-08T09:02:41] Filtering duplicates (remaining=6027618)
[2026-06-08T09:02:50] 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=5873632)
[2026-06-08T09:02:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5873632)
[2026-06-08T09:02:55] Filtering viral contigs with expression lower than the top 5 (remaining=5873632)
[2026-06-08T09:03:01] Filtering viral contigs with less than 5% coverage (remaining=5873632)
[2026-06-08T09:03:04] Estimating fragment length (mate gap mean=-88.9933, mate gap stddev=28.9198, read length mean=138.22)
[2026-06-08T09:03:04] Filtering read-through fragments with a distance <=10000bp (remaining=5549373)
[2026-06-08T09:03:06] Filtering inconsistently clipped mates (remaining=5485729)
[2026-06-08T09:03:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5311879)
[2026-06-08T09:03:14] Filtering fragments with small insert size (remaining=5311335)
[2026-06-08T09:03:16] Filtering alignments with long gaps (remaining=5311335)
[2026-06-08T09:03:19] Filtering fragments with both mates in the same gene (remaining=5310495)
[2026-06-08T09:03:24] Filtering fusions arising from hairpin structures (remaining=5081321)
[2026-06-08T09:03:27] Filtering reads with a mismatch p-value <=0.01 (remaining=2537676)
[2026-06-08T09:03:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=866937)
[2026-06-08T09:03:52] Finding fusions and counting supporting reads (total=680050)
[2026-06-08T09:04:12] Merging adjacent fusion breakpoints (remaining=674585)
[2026-06-08T09:04:13] Filtering multi-mapping fusions by alignment score and read support (remaining=440305)
[2026-06-08T09:04:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:05:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=438195)
[2026-06-08T09:05:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=224776)
[2026-06-08T09:05:03] Filtering fusions with <2 supporting reads (remaining=32104)
[2026-06-08T09:05:04] Filtering fusions with an e-value >=0.3 (remaining=10035)
[2026-06-08T09:05:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10072)
[2026-06-08T09:05:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9995)
[2026-06-08T09:05:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9996)
[2026-06-08T09:05:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6679)
[2026-06-08T09:05:16] Searching for fusions with spliced split reads (remaining=6785)
[2026-06-08T09:05:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=4062)
[2026-06-08T09:05:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4007)
[2026-06-08T09:05:24] Searching for fusions with >=4 spliced events (remaining=4749)
[2026-06-08T09:05:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1510)
[2026-06-08T09:05:38] Filtering fusions with anchors <=23nt (remaining=1215)
[2026-06-08T09:05:39] Filtering end-to-end fusions with low support (remaining=1172)
[2026-06-08T09:05:40] Filtering fusions with no coverage around the breakpoints (remaining=1142)
[2026-06-08T09:05:40] Indexing gene sequences 
[2026-06-08T09:05:46] Filtering genes with >=30% identity (remaining=352)
[2026-06-08T09:05:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=161)
[2026-06-08T09:05:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=155)
[2026-06-08T09:05:54] Searching for additional isoforms (remaining=198)
[2026-06-08T09:05:55] Assigning confidence scores to events 
[2026-06-08T09:05:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:59] Writing fusions to file '659_bNS-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:06:00] Writing discarded fusions to file '659_bNS-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:31] Freeing resources
[2026-06-08T09:06:52] Done (elapsed time=00:12:17, CPU time=00:12:15, peak memory=16gb)