[2026-05-28T00:04:40] Launching Arriba 2.4.0
[2026-05-28T00:04:40] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:04:48] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:52] Reading chimeric alignments from '659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3304224)
[2026-05-28T00:07:08] Marking multi-mapping alignments (marked=2074653)
[2026-05-28T00:07:09] Detecting strandedness (reverse)
[2026-05-28T00:07:09] Assigning strands to alignments 
[2026-05-28T00:07:10] Annotating alignments 
[2026-05-28T00:07:23] Filtering duplicates (remaining=1732468)
[2026-05-28T00:07:25] 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=1638770)
[2026-05-28T00:07:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1638770)
[2026-05-28T00:07:26] Filtering viral contigs with expression lower than the top 5 (remaining=1638770)
[2026-05-28T00:07:27] Filtering viral contigs with less than 5% coverage (remaining=1638770)
[2026-05-28T00:07:28] Estimating fragment length (mate gap mean=-88.8594, mate gap stddev=28.3627, read length mean=133.15)
[2026-05-28T00:07:28] Filtering read-through fragments with a distance <=10000bp (remaining=1542430)
[2026-05-28T00:07:29] Filtering inconsistently clipped mates (remaining=1512023)
[2026-05-28T00:07:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1456617)
[2026-05-28T00:07:31] Filtering fragments with small insert size (remaining=1456363)
[2026-05-28T00:07:32] Filtering alignments with long gaps (remaining=1456363)
[2026-05-28T00:07:32] Filtering fragments with both mates in the same gene (remaining=1455999)
[2026-05-28T00:07:33] Filtering fusions arising from hairpin structures (remaining=1368333)
[2026-05-28T00:07:34] Filtering reads with a mismatch p-value <=0.01 (remaining=578292)
[2026-05-28T00:07:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=246580)
[2026-05-28T00:07:41] Finding fusions and counting supporting reads (total=210460)
[2026-05-28T00:07:47] Merging adjacent fusion breakpoints (remaining=208927)
[2026-05-28T00:07:48] Filtering multi-mapping fusions by alignment score and read support (remaining=135873)
[2026-05-28T00:08:00] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=134995)
[2026-05-28T00:08:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=69955)
[2026-05-28T00:08:03] Filtering fusions with <2 supporting reads (remaining=8627)
[2026-05-28T00:08:03] Filtering fusions with an e-value >=0.3 (remaining=2678)
[2026-05-28T00:08:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2703)
[2026-05-28T00:08:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2676)
[2026-05-28T00:08:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2678)
[2026-05-28T00:08:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1878)
[2026-05-28T00:08:07] Searching for fusions with spliced split reads (remaining=2004)
[2026-05-28T00:08:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=1440)
[2026-05-28T00:08:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1430)
[2026-05-28T00:08:09] Searching for fusions with >=4 spliced events (remaining=1556)
[2026-05-28T00:08:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=414)
[2026-05-28T00:08:21] Filtering fusions with anchors <=23nt (remaining=339)
[2026-05-28T00:08:21] Filtering end-to-end fusions with low support (remaining=329)
[2026-05-28T00:08:21] Filtering fusions with no coverage around the breakpoints (remaining=322)
[2026-05-28T00:08:21] Indexing gene sequences 
[2026-05-28T00:08:24] Filtering genes with >=30% identity (remaining=104)
[2026-05-28T00:08:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=53)
[2026-05-28T00:08:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=45)
[2026-05-28T00:08:25] Searching for additional isoforms (remaining=62)
[2026-05-28T00:08:26] Assigning confidence scores to events 
[2026-05-28T00:08:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:27] Writing fusions to file '659_bua-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:08:28] Writing discarded fusions to file '659_bua-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:38] Freeing resources
[2026-05-28T00:08:44] Done (elapsed time=00:04:04, CPU time=00:04:04, peak memory=7.59gb)