[2026-06-08T08:21:08] Launching Arriba 2.4.0
[2026-06-08T08:21:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:21:28] Reading chimeric alignments from '659_Lx-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9259575)
[2026-06-08T08:28:00] Marking multi-mapping alignments (marked=5833675)
[2026-06-08T08:28:04] Detecting strandedness (no)
[2026-06-08T08:28:04] Annotating alignments 
[2026-06-08T08:28:41] Filtering duplicates (remaining=3307102)
[2026-06-08T08:28:46] 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=3118104)
[2026-06-08T08:28:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3118104)
[2026-06-08T08:28:49] Filtering viral contigs with expression lower than the top 5 (remaining=3118104)
[2026-06-08T08:28:53] Filtering viral contigs with less than 5% coverage (remaining=3118104)
[2026-06-08T08:28:55] Estimating fragment length (mate gap mean=-85.8067, mate gap stddev=27.6676, read length mean=125.297)
[2026-06-08T08:28:55] Filtering read-through fragments with a distance <=10000bp (remaining=2916983)
[2026-06-08T08:28:57] Filtering inconsistently clipped mates (remaining=2870122)
[2026-06-08T08:28:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2778329)
[2026-06-08T08:29:02] Filtering fragments with small insert size (remaining=2777571)
[2026-06-08T08:29:04] Filtering alignments with long gaps (remaining=2777571)
[2026-06-08T08:29:06] Filtering fragments with both mates in the same gene (remaining=2776829)
[2026-06-08T08:29:08] Filtering fusions arising from hairpin structures (remaining=2663789)
[2026-06-08T08:29:10] Filtering reads with a mismatch p-value <=0.01 (remaining=1076858)
[2026-06-08T08:29:17] Filtering reads with low entropy (k-mer content >=60%) (remaining=470444)
[2026-06-08T08:29:24] Finding fusions and counting supporting reads (total=409008)
[2026-06-08T08:29:36] Merging adjacent fusion breakpoints (remaining=404891)
[2026-06-08T08:29:37] Filtering multi-mapping fusions by alignment score and read support (remaining=242770)
[2026-06-08T08:30:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:30:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=241931)
[2026-06-08T08:30:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=126255)
[2026-06-08T08:30:10] Filtering fusions with <2 supporting reads (remaining=14056)
[2026-06-08T08:30:10] Filtering fusions with an e-value >=0.3 (remaining=3493)
[2026-06-08T08:30:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3514)
[2026-06-08T08:30:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3465)
[2026-06-08T08:30:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3466)
[2026-06-08T08:30:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3398)
[2026-06-08T08:30:18] Searching for fusions with spliced split reads (remaining=3415)
[2026-06-08T08:30:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=2373)
[2026-06-08T08:30:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2356)
[2026-06-08T08:30:23] Searching for fusions with >=4 spliced events (remaining=2632)
[2026-06-08T08:30:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=776)
[2026-06-08T08:30:39] Filtering fusions with anchors <=23nt (remaining=656)
[2026-06-08T08:30:39] Filtering end-to-end fusions with low support (remaining=635)
[2026-06-08T08:30:39] Filtering fusions with no coverage around the breakpoints (remaining=621)
[2026-06-08T08:30:40] Indexing gene sequences 
[2026-06-08T08:30:43] Filtering genes with >=30% identity (remaining=228)
[2026-06-08T08:30:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=85)
[2026-06-08T08:30:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=82)
[2026-06-08T08:30:46] Searching for additional isoforms (remaining=89)
[2026-06-08T08:30:47] Assigning confidence scores to events 
[2026-06-08T08:30:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:49] Writing fusions to file '659_Lx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:30:49] Writing discarded fusions to file '659_Lx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:31:07] Freeing resources
[2026-06-08T08:31:22] Done (elapsed time=00:10:14, CPU time=00:10:13, peak memory=13.6gb)