[2026-05-27T23:59:39] Launching Arriba 2.4.0
[2026-05-27T23:59:39] Loading assembly from 'ref_genome.fa' 
[2026-05-27T23:59:52] Loading annotation from 'ref_annot.gtf' 
[2026-05-27T23:59:58] Reading chimeric alignments from '659_bNS-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3607407)
[2026-05-28T00:03:08] Marking multi-mapping alignments (marked=2296787)
[2026-05-28T00:03:10] Detecting strandedness (reverse)
[2026-05-28T00:03:10] Assigning strands to alignments 
[2026-05-28T00:03:10] Annotating alignments 
[2026-05-28T00:03:27] Filtering duplicates (remaining=1928675)
[2026-05-28T00:03:31] 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=1816447)
[2026-05-28T00:03:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1816447)
[2026-05-28T00:03:33] Filtering viral contigs with expression lower than the top 5 (remaining=1816447)
[2026-05-28T00:03:35] Filtering viral contigs with less than 5% coverage (remaining=1816447)
[2026-05-28T00:03:37] Estimating fragment length (mate gap mean=-87.8963, mate gap stddev=29.4685, read length mean=134.4)
[2026-05-28T00:03:37] Filtering read-through fragments with a distance <=10000bp (remaining=1711226)
[2026-05-28T00:03:38] Filtering inconsistently clipped mates (remaining=1685362)
[2026-05-28T00:03:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1634988)
[2026-05-28T00:03:41] Filtering fragments with small insert size (remaining=1634749)
[2026-05-28T00:03:42] Filtering alignments with long gaps (remaining=1634749)
[2026-05-28T00:03:43] Filtering fragments with both mates in the same gene (remaining=1634434)
[2026-05-28T00:03:44] Filtering fusions arising from hairpin structures (remaining=1542214)
[2026-05-28T00:03:45] Filtering reads with a mismatch p-value <=0.01 (remaining=650503)
[2026-05-28T00:03:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=281074)
[2026-05-28T00:03:55] Finding fusions and counting supporting reads (total=237001)
[2026-05-28T00:04:04] Merging adjacent fusion breakpoints (remaining=235100)
[2026-05-28T00:04:04] Filtering multi-mapping fusions by alignment score and read support (remaining=151831)
[2026-05-28T00:04:23] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:04:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=150937)
[2026-05-28T00:04:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=77801)
[2026-05-28T00:04:27] Filtering fusions with <2 supporting reads (remaining=10240)
[2026-05-28T00:04:27] Filtering fusions with an e-value >=0.3 (remaining=3271)
[2026-05-28T00:04:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3294)
[2026-05-28T00:04:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3256)
[2026-05-28T00:04:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3256)
[2026-05-28T00:04:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2411)
[2026-05-28T00:04:32] Searching for fusions with spliced split reads (remaining=2506)
[2026-05-28T00:04:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=1803)
[2026-05-28T00:04:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1791)
[2026-05-28T00:04:35] Searching for fusions with >=4 spliced events (remaining=1924)
[2026-05-28T00:04:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=528)
[2026-05-28T00:04:54] Filtering fusions with anchors <=23nt (remaining=407)
[2026-05-28T00:04:55] Filtering end-to-end fusions with low support (remaining=389)
[2026-05-28T00:04:55] Filtering fusions with no coverage around the breakpoints (remaining=376)
[2026-05-28T00:04:55] Indexing gene sequences 
[2026-05-28T00:04:59] Filtering genes with >=30% identity (remaining=163)
[2026-05-28T00:05:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=107)
[2026-05-28T00:05:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=107)
[2026-05-28T00:05:02] Searching for additional isoforms (remaining=122)
[2026-05-28T00:05:03] Assigning confidence scores to events 
[2026-05-28T00:05:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:05:05] Writing fusions to file '659_bNS-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:05:06] Writing discarded fusions to file '659_bNS-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:05:20] Freeing resources
[2026-05-28T00:05:31] Done (elapsed time=00:05:52, CPU time=00:05:51, peak memory=7.94gb)