[2026-06-08T07:43:56] Launching Arriba 2.4.0
[2026-06-08T07:43:56] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:44:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:44:17] Reading chimeric alignments from '659_dcz-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=3041797)
[2026-06-08T07:46:39] Marking multi-mapping alignments (marked=2060277)
[2026-06-08T07:46:40] Detecting strandedness (reverse)
[2026-06-08T07:46:40] Assigning strands to alignments 
[2026-06-08T07:46:41] Annotating alignments 
[2026-06-08T07:46:53] Filtering duplicates (remaining=906196)
[2026-06-08T07:46:55] 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=854387)
[2026-06-08T07:46:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=854387)
[2026-06-08T07:46:56] Filtering viral contigs with expression lower than the top 5 (remaining=854387)
[2026-06-08T07:46:57] Filtering viral contigs with less than 5% coverage (remaining=854387)
[2026-06-08T07:46:58] Estimating fragment length (mate gap mean=-84.5892, mate gap stddev=27.2393, read length mean=122.149)
[2026-06-08T07:46:58] Filtering read-through fragments with a distance <=10000bp (remaining=820473)
[2026-06-08T07:46:59] Filtering inconsistently clipped mates (remaining=802637)
[2026-06-08T07:46:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=739189)
[2026-06-08T07:47:00] Filtering fragments with small insert size (remaining=738954)
[2026-06-08T07:47:01] Filtering alignments with long gaps (remaining=738954)
[2026-06-08T07:47:01] Filtering fragments with both mates in the same gene (remaining=738736)
[2026-06-08T07:47:02] Filtering fusions arising from hairpin structures (remaining=704361)
[2026-06-08T07:47:02] Filtering reads with a mismatch p-value <=0.01 (remaining=287936)
[2026-06-08T07:47:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=94926)
[2026-06-08T07:47:07] Finding fusions and counting supporting reads (total=95160)
[2026-06-08T07:47:11] Merging adjacent fusion breakpoints (remaining=94838)
[2026-06-08T07:47:12] Filtering multi-mapping fusions by alignment score and read support (remaining=42854)
[2026-06-08T07:47:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:47:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=42453)
[2026-06-08T07:47:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=28426)
[2026-06-08T07:47:25] Filtering fusions with <2 supporting reads (remaining=1478)
[2026-06-08T07:47:25] Filtering fusions with an e-value >=0.3 (remaining=418)
[2026-06-08T07:47:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=425)
[2026-06-08T07:47:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=398)
[2026-06-08T07:47:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=398)
[2026-06-08T07:47:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=395)
[2026-06-08T07:47:27] Searching for fusions with spliced split reads (remaining=432)
[2026-06-08T07:47:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=365)
[2026-06-08T07:47:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=359)
[2026-06-08T07:47:28] Searching for fusions with >=4 spliced events (remaining=384)
[2026-06-08T07:47:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=132)
[2026-06-08T07:47:51] Filtering fusions with anchors <=23nt (remaining=116)
[2026-06-08T07:47:51] Filtering end-to-end fusions with low support (remaining=111)
[2026-06-08T07:47:51] Filtering fusions with no coverage around the breakpoints (remaining=105)
[2026-06-08T07:47:51] Indexing gene sequences 
[2026-06-08T07:47:52] Filtering genes with >=30% identity (remaining=41)
[2026-06-08T07:47:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=28)
[2026-06-08T07:47:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=28)
[2026-06-08T07:47:53] Searching for additional isoforms (remaining=32)
[2026-06-08T07:47:53] Assigning confidence scores to events 
[2026-06-08T07:47:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:47:54] Writing fusions to file '659_dcz-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T07:47:54] Writing discarded fusions to file '659_dcz-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T07:48:01] Freeing resources
[2026-06-08T07:48:08] Done (elapsed time=00:04:12, CPU time=00:04:11, peak memory=7.19gb)