[2026-05-28T00:06:42] Launching Arriba 2.4.0
[2026-05-28T00:06:42] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:06:51] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:06:56] Reading chimeric alignments from '659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3219536)
[2026-05-28T00:09:30] Marking multi-mapping alignments (marked=1962127)
[2026-05-28T00:09:31] Detecting strandedness (reverse)
[2026-05-28T00:09:31] Assigning strands to alignments 
[2026-05-28T00:09:32] Annotating alignments 
[2026-05-28T00:09:44] Filtering duplicates (remaining=2164774)
[2026-05-28T00:09:47] 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=2064145)
[2026-05-28T00:09:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2064145)
[2026-05-28T00:09:48] Filtering viral contigs with expression lower than the top 5 (remaining=2064145)
[2026-05-28T00:09:50] Filtering viral contigs with less than 5% coverage (remaining=2064145)
[2026-05-28T00:09:51] Estimating fragment length (mate gap mean=-88.5526, mate gap stddev=29.6383, read length mean=136.773)
[2026-05-28T00:09:51] Filtering read-through fragments with a distance <=10000bp (remaining=1930759)
[2026-05-28T00:09:51] Filtering inconsistently clipped mates (remaining=1900901)
[2026-05-28T00:09:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1854640)
[2026-05-28T00:09:54] Filtering fragments with small insert size (remaining=1854395)
[2026-05-28T00:09:54] Filtering alignments with long gaps (remaining=1854395)
[2026-05-28T00:09:55] Filtering fragments with both mates in the same gene (remaining=1854084)
[2026-05-28T00:09:56] Filtering fusions arising from hairpin structures (remaining=1747387)
[2026-05-28T00:09:57] Filtering reads with a mismatch p-value <=0.01 (remaining=782685)
[2026-05-28T00:10:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=333572)
[2026-05-28T00:10:05] Finding fusions and counting supporting reads (total=274741)
[2026-05-28T00:10:12] Merging adjacent fusion breakpoints (remaining=272483)
[2026-05-28T00:10:12] Filtering multi-mapping fusions by alignment score and read support (remaining=193124)
[2026-05-28T00:10:25] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:10:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=192284)
[2026-05-28T00:10:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=93519)
[2026-05-28T00:10:28] Filtering fusions with <2 supporting reads (remaining=14326)
[2026-05-28T00:10:29] Filtering fusions with an e-value >=0.3 (remaining=5403)
[2026-05-28T00:10:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5436)
[2026-05-28T00:10:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5421)
[2026-05-28T00:10:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5421)
[2026-05-28T00:10:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2939)
[2026-05-28T00:10:33] Searching for fusions with spliced split reads (remaining=2986)
[2026-05-28T00:10:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=2024)
[2026-05-28T00:10:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2015)
[2026-05-28T00:10:36] Searching for fusions with >=4 spliced events (remaining=2192)
[2026-05-28T00:10:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=651)
[2026-05-28T00:10:48] Filtering fusions with anchors <=23nt (remaining=493)
[2026-05-28T00:10:48] Filtering end-to-end fusions with low support (remaining=476)
[2026-05-28T00:10:49] Filtering fusions with no coverage around the breakpoints (remaining=459)
[2026-05-28T00:10:49] Indexing gene sequences 
[2026-05-28T00:10:51] Filtering genes with >=30% identity (remaining=203)
[2026-05-28T00:10:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=133)
[2026-05-28T00:10:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=124)
[2026-05-28T00:10:55] Searching for additional isoforms (remaining=146)
[2026-05-28T00:10:55] Assigning confidence scores to events 
[2026-05-28T00:10:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:10:57] Writing fusions to file '659_bTo-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:10:58] Writing discarded fusions to file '659_bTo-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:11:11] Freeing resources
[2026-05-28T00:11:18] Done (elapsed time=00:04:36, CPU time=00:04:35, peak memory=7.54gb)