[2026-06-08T08:10:54] Launching Arriba 2.4.0
[2026-06-08T08:10:54] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:11:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:11:08] Reading chimeric alignments from '659_Dl-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=6293782)
[2026-06-08T08:14:23] Marking multi-mapping alignments (marked=4381680)
[2026-06-08T08:14:26] Detecting strandedness (reverse)
[2026-06-08T08:14:26] Assigning strands to alignments 
[2026-06-08T08:14:27] Annotating alignments 
[2026-06-08T08:14:47] Filtering duplicates (remaining=1543556)
[2026-06-08T08:14:50] 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=1341417)
[2026-06-08T08:14:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1341417)
[2026-06-08T08:14:52] Filtering viral contigs with expression lower than the top 5 (remaining=1341417)
[2026-06-08T08:14:54] Filtering viral contigs with less than 5% coverage (remaining=1341417)
[2026-06-08T08:14:56] Estimating fragment length (mate gap mean=-86.5058, mate gap stddev=27.6893, read length mean=125.835)
[2026-06-08T08:14:56] Filtering read-through fragments with a distance <=10000bp (remaining=1291525)
[2026-06-08T08:14:57] Filtering inconsistently clipped mates (remaining=1262454)
[2026-06-08T08:14:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1175284)
[2026-06-08T08:15:00] Filtering fragments with small insert size (remaining=1174931)
[2026-06-08T08:15:01] Filtering alignments with long gaps (remaining=1174931)
[2026-06-08T08:15:02] Filtering fragments with both mates in the same gene (remaining=1174585)
[2026-06-08T08:15:03] Filtering fusions arising from hairpin structures (remaining=1117368)
[2026-06-08T08:15:04] Filtering reads with a mismatch p-value <=0.01 (remaining=421397)
[2026-06-08T08:15:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=152105)
[2026-06-08T08:15:11] Finding fusions and counting supporting reads (total=139746)
[2026-06-08T08:15:19] Merging adjacent fusion breakpoints (remaining=138507)
[2026-06-08T08:15:19] Filtering multi-mapping fusions by alignment score and read support (remaining=64069)
[2026-06-08T08:15:37] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:15:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=63295)
[2026-06-08T08:15:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=41465)
[2026-06-08T08:15:40] Filtering fusions with <2 supporting reads (remaining=3168)
[2026-06-08T08:15:40] Filtering fusions with an e-value >=0.3 (remaining=895)
[2026-06-08T08:15:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=904)
[2026-06-08T08:15:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=851)
[2026-06-08T08:15:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=851)
[2026-06-08T08:15:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=828)
[2026-06-08T08:15:44] Searching for fusions with spliced split reads (remaining=954)
[2026-06-08T08:15:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=732)
[2026-06-08T08:15:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=726)
[2026-06-08T08:15:47] Searching for fusions with >=4 spliced events (remaining=778)
[2026-06-08T08:15:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=257)
[2026-06-08T08:15:58] Filtering fusions with anchors <=23nt (remaining=216)
[2026-06-08T08:15:58] Filtering end-to-end fusions with low support (remaining=211)
[2026-06-08T08:15:59] Filtering fusions with no coverage around the breakpoints (remaining=202)
[2026-06-08T08:15:59] Indexing gene sequences 
[2026-06-08T08:16:01] Filtering genes with >=30% identity (remaining=85)
[2026-06-08T08:16:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=54)
[2026-06-08T08:16:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=51)
[2026-06-08T08:16:02] Searching for additional isoforms (remaining=60)
[2026-06-08T08:16:02] Assigning confidence scores to events 
[2026-06-08T08:16:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:16:03] Writing fusions to file '659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:16:04] Writing discarded fusions to file '659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:16:11] Freeing resources
[2026-06-08T08:16:20] Done (elapsed time=00:05:26, CPU time=00:05:25, peak memory=10.6gb)