[2026-05-28T00:04:45] Launching Arriba 2.4.0
[2026-05-28T00:04:45] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:04:53] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:57] Reading chimeric alignments from '659_dc8-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3587809)
[2026-05-28T00:07:18] Marking multi-mapping alignments (marked=2249298)
[2026-05-28T00:07:20] Detecting strandedness (reverse)
[2026-05-28T00:07:20] Assigning strands to alignments 
[2026-05-28T00:07:21] Annotating alignments 
[2026-05-28T00:07:34] Filtering duplicates (remaining=1869896)
[2026-05-28T00:07:37] 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=1787071)
[2026-05-28T00:07:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1787071)
[2026-05-28T00:07:39] Filtering viral contigs with expression lower than the top 5 (remaining=1787071)
[2026-05-28T00:07:41] Filtering viral contigs with less than 5% coverage (remaining=1787071)
[2026-05-28T00:07:42] Estimating fragment length (mate gap mean=-86.5361, mate gap stddev=29.5699, read length mean=134.117)
[2026-05-28T00:07:42] Filtering read-through fragments with a distance <=10000bp (remaining=1677086)
[2026-05-28T00:07:43] Filtering inconsistently clipped mates (remaining=1651448)
[2026-05-28T00:07:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1599580)
[2026-05-28T00:07:45] Filtering fragments with small insert size (remaining=1599341)
[2026-05-28T00:07:46] Filtering alignments with long gaps (remaining=1599341)
[2026-05-28T00:07:47] Filtering fragments with both mates in the same gene (remaining=1599024)
[2026-05-28T00:07:48] Filtering fusions arising from hairpin structures (remaining=1518337)
[2026-05-28T00:07:49] Filtering reads with a mismatch p-value <=0.01 (remaining=679278)
[2026-05-28T00:07:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=271017)
[2026-05-28T00:07:56] Finding fusions and counting supporting reads (total=243878)
[2026-05-28T00:08:04] Merging adjacent fusion breakpoints (remaining=241992)
[2026-05-28T00:08:05] Filtering multi-mapping fusions by alignment score and read support (remaining=147827)
[2026-05-28T00:08:20] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=146335)
[2026-05-28T00:08:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=74272)
[2026-05-28T00:08:23] Filtering fusions with <2 supporting reads (remaining=9758)
[2026-05-28T00:08:23] Filtering fusions with an e-value >=0.3 (remaining=3455)
[2026-05-28T00:08:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3485)
[2026-05-28T00:08:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3451)
[2026-05-28T00:08:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3452)
[2026-05-28T00:08:25] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2491)
[2026-05-28T00:08:27] Searching for fusions with spliced split reads (remaining=2609)
[2026-05-28T00:08:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=1798)
[2026-05-28T00:08:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1781)
[2026-05-28T00:08:30] Searching for fusions with >=4 spliced events (remaining=1944)
[2026-05-28T00:08:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=502)
[2026-05-28T00:08:43] Filtering fusions with anchors <=23nt (remaining=377)
[2026-05-28T00:08:43] Filtering end-to-end fusions with low support (remaining=362)
[2026-05-28T00:08:43] Filtering fusions with no coverage around the breakpoints (remaining=347)
[2026-05-28T00:08:44] Indexing gene sequences 
[2026-05-28T00:08:46] Filtering genes with >=30% identity (remaining=120)
[2026-05-28T00:08:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=78)
[2026-05-28T00:08:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=62)
[2026-05-28T00:08:49] Searching for additional isoforms (remaining=84)
[2026-05-28T00:08:49] Assigning confidence scores to events 
[2026-05-28T00:08:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:50] Writing fusions to file '659_dc8-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:08:51] Writing discarded fusions to file '659_dc8-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:03] Freeing resources
[2026-05-28T00:09:12] Done (elapsed time=00:04:27, CPU time=00:04:26, peak memory=7.83gb)