[2026-05-27T23:55:58] Launching Arriba 2.4.0
[2026-05-27T23:55:58] Loading assembly from 'ref_genome.fa' 
[2026-05-27T23:56:07] Loading annotation from 'ref_annot.gtf' 
[2026-05-27T23:56:11] Reading chimeric alignments from '659_Lx-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3645136)
[2026-05-27T23:58:20] Marking multi-mapping alignments (marked=2292774)
[2026-05-27T23:58:21] Detecting strandedness (reverse)
[2026-05-27T23:58:21] Assigning strands to alignments 
[2026-05-27T23:58:22] Annotating alignments 
[2026-05-27T23:58:34] Filtering duplicates (remaining=1908914)
[2026-05-27T23:58:37] 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=1806097)
[2026-05-27T23:58:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1806097)
[2026-05-27T23:58:38] Filtering viral contigs with expression lower than the top 5 (remaining=1806097)
[2026-05-27T23:58:39] Filtering viral contigs with less than 5% coverage (remaining=1806097)
[2026-05-27T23:58:40] Estimating fragment length (mate gap mean=-86.3062, mate gap stddev=27.0334, read length mean=125.429)
[2026-05-27T23:58:41] Filtering read-through fragments with a distance <=10000bp (remaining=1666471)
[2026-05-27T23:58:41] Filtering inconsistently clipped mates (remaining=1637762)
[2026-05-27T23:58:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1596109)
[2026-05-27T23:58:43] Filtering fragments with small insert size (remaining=1595685)
[2026-05-27T23:58:44] Filtering alignments with long gaps (remaining=1595685)
[2026-05-27T23:58:45] Filtering fragments with both mates in the same gene (remaining=1595293)
[2026-05-27T23:58:45] Filtering fusions arising from hairpin structures (remaining=1517513)
[2026-05-27T23:58:46] Filtering reads with a mismatch p-value <=0.01 (remaining=646110)
[2026-05-27T23:58:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=311136)
[2026-05-27T23:58:53] Finding fusions and counting supporting reads (total=274645)
[2026-05-27T23:59:00] Merging adjacent fusion breakpoints (remaining=272548)
[2026-05-27T23:59:00] Filtering multi-mapping fusions by alignment score and read support (remaining=169051)
[2026-05-27T23:59:12] Estimating expected number of fusions by random chance (e-value) 
[2026-05-27T23:59:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=168515)
[2026-05-27T23:59:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=84593)
[2026-05-27T23:59:15] Filtering fusions with <2 supporting reads (remaining=9723)
[2026-05-27T23:59:15] Filtering fusions with an e-value >=0.3 (remaining=2686)
[2026-05-27T23:59:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2707)
[2026-05-27T23:59:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2683)
[2026-05-27T23:59:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2683)
[2026-05-27T23:59:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2631)
[2026-05-27T23:59:19] Searching for fusions with spliced split reads (remaining=2714)
[2026-05-27T23:59:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=1953)
[2026-05-27T23:59:21] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1940)
[2026-05-27T23:59:21] Searching for fusions with >=4 spliced events (remaining=2102)
[2026-05-27T23:59:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=561)
[2026-05-27T23:59:33] Filtering fusions with anchors <=23nt (remaining=470)
[2026-05-27T23:59:33] Filtering end-to-end fusions with low support (remaining=459)
[2026-05-27T23:59:33] Filtering fusions with no coverage around the breakpoints (remaining=449)
[2026-05-27T23:59:34] Indexing gene sequences 
[2026-05-27T23:59:36] Filtering genes with >=30% identity (remaining=163)
[2026-05-27T23:59:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=77)
[2026-05-27T23:59:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=74)
[2026-05-27T23:59:38] Searching for additional isoforms (remaining=81)
[2026-05-27T23:59:38] Assigning confidence scores to events 
[2026-05-27T23:59:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-27T23:59:39] Writing fusions to file '659_Lx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-27T23:59:40] Writing discarded fusions to file '659_Lx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-27T23:59:50] Freeing resources
[2026-05-27T23:59:58] Done (elapsed time=00:04:00, CPU time=00:03:59, peak memory=7.92gb)