[2026-06-04T20:29:58] Launching Arriba 2.4.0
[2026-06-04T20:29:58] Loading assembly from 'ref_genome.fa' 
[2026-06-04T20:30:06] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T20:30:10] Reading chimeric alignments from '659_b4x-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=3910996)
[2026-06-04T20:31:38] Marking multi-mapping alignments (marked=2851650)
[2026-06-04T20:31:40] Detecting strandedness (no)
[2026-06-04T20:31:40] Annotating alignments 
[2026-06-04T20:31:52] Filtering duplicates (remaining=1067324)
[2026-06-04T20:31:53] 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=884520)
[2026-06-04T20:31:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=884520)
[2026-06-04T20:31:54] Filtering viral contigs with expression lower than the top 5 (remaining=884520)
[2026-06-04T20:31:55] Filtering viral contigs with less than 5% coverage (remaining=884520)
[2026-06-04T20:31:56] Estimating fragment length (mate gap mean=-77.5311, mate gap stddev=28.4518, read length mean=111.113)
[2026-06-04T20:31:56] Filtering read-through fragments with a distance <=10000bp (remaining=858546)
[2026-06-04T20:31:57] Filtering inconsistently clipped mates (remaining=832853)
[2026-06-04T20:31:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=784843)
[2026-06-04T20:31:59] Filtering fragments with small insert size (remaining=784253)
[2026-06-04T20:31:59] Filtering alignments with long gaps (remaining=784253)
[2026-06-04T20:32:00] Filtering fragments with both mates in the same gene (remaining=783784)
[2026-06-04T20:32:00] Filtering fusions arising from hairpin structures (remaining=735733)
[2026-06-04T20:32:01] Filtering reads with a mismatch p-value <=0.01 (remaining=246445)
[2026-06-04T20:32:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=83149)
[2026-06-04T20:32:05] Finding fusions and counting supporting reads (total=75435)
[2026-06-04T20:32:08] Merging adjacent fusion breakpoints (remaining=74959)
[2026-06-04T20:32:08] Filtering multi-mapping fusions by alignment score and read support (remaining=38479)
[2026-06-04T20:32:17] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T20:32:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=38015)
[2026-06-04T20:32:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=24483)
[2026-06-04T20:32:18] Filtering fusions with <2 supporting reads (remaining=1362)
[2026-06-04T20:32:18] Filtering fusions with an e-value >=0.3 (remaining=453)
[2026-06-04T20:32:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=465)
[2026-06-04T20:32:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=436)
[2026-06-04T20:32:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=436)
[2026-06-04T20:32:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=428)
[2026-06-04T20:32:21] Searching for fusions with spliced split reads (remaining=467)
[2026-06-04T20:32:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=376)
[2026-06-04T20:32:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=368)
[2026-06-04T20:32:22] Searching for fusions with >=4 spliced events (remaining=378)
[2026-06-04T20:32:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=120)
[2026-06-04T20:32:32] Filtering fusions with anchors <=23nt (remaining=90)
[2026-06-04T20:32:32] Filtering end-to-end fusions with low support (remaining=74)
[2026-06-04T20:32:32] Filtering fusions with no coverage around the breakpoints (remaining=67)
[2026-06-04T20:32:32] Indexing gene sequences 
[2026-06-04T20:32:33] Filtering genes with >=30% identity (remaining=28)
[2026-06-04T20:32:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=12)
[2026-06-04T20:32:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=12)
[2026-06-04T20:32:34] Searching for additional isoforms (remaining=13)
[2026-06-04T20:32:34] Assigning confidence scores to events 
[2026-06-04T20:32:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T20:32:34] Writing fusions to file '659_b4x-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T20:32:34] Writing discarded fusions to file '659_b4x-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T20:32:38] Freeing resources
[2026-06-04T20:32:43] Done (elapsed time=00:02:45, CPU time=00:02:44, peak memory=8.08gb)