[2026-06-08T08:59:20] Launching Arriba 2.4.0
[2026-06-08T08:59:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:59:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:59:34] Reading chimeric alignments from 'FFPE_HD789_01_RNA_13_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9700542)
[2026-06-08T09:07:00] Marking multi-mapping alignments (marked=6206070)
[2026-06-08T09:07:05] Detecting strandedness (reverse)
[2026-06-08T09:07:05] Assigning strands to alignments 
[2026-06-08T09:07:07] Annotating alignments 
[2026-06-08T09:07:43] Filtering duplicates (remaining=6677741)
[2026-06-08T09:07:51] 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=6323891)
[2026-06-08T09:07:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6323891)
[2026-06-08T09:07:55] Filtering viral contigs with expression lower than the top 5 (remaining=6323891)
[2026-06-08T09:07:59] Filtering viral contigs with less than 5% coverage (remaining=6323891)
[2026-06-08T09:08:02] Estimating fragment length (mate gap mean=-83.2104, mate gap stddev=33.5501, read length mean=138.66)
[2026-06-08T09:08:02] Filtering read-through fragments with a distance <=10000bp (remaining=6052563)
[2026-06-08T09:08:04] Filtering inconsistently clipped mates (remaining=5967519)
[2026-06-08T09:08:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5761735)
[2026-06-08T09:08:11] Filtering fragments with small insert size (remaining=5761209)
[2026-06-08T09:08:13] Filtering alignments with long gaps (remaining=5761209)
[2026-06-08T09:08:15] Filtering fragments with both mates in the same gene (remaining=5760110)
[2026-06-08T09:08:17] Filtering fusions arising from hairpin structures (remaining=5395624)
[2026-06-08T09:08:19] Filtering reads with a mismatch p-value <=0.01 (remaining=2735318)
[2026-06-08T09:08:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=992160)
[2026-06-08T09:08:45] Finding fusions and counting supporting reads (total=733201)
[2026-06-08T09:09:03] Merging adjacent fusion breakpoints (remaining=726391)
[2026-06-08T09:09:04] Filtering multi-mapping fusions by alignment score and read support (remaining=480263)
[2026-06-08T09:09:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:09:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=475039)
[2026-06-08T09:09:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=275856)
[2026-06-08T09:09:48] Filtering fusions with <2 supporting reads (remaining=44042)
[2026-06-08T09:09:49] Filtering fusions with an e-value >=0.3 (remaining=18057)
[2026-06-08T09:09:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=18111)
[2026-06-08T09:09:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=17993)
[2026-06-08T09:09:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17999)
[2026-06-08T09:09:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10077)
[2026-06-08T09:10:00] Searching for fusions with spliced split reads (remaining=10102)
[2026-06-08T09:10:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=5038)
[2026-06-08T09:10:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4998)
[2026-06-08T09:10:07] Searching for fusions with >=4 spliced events (remaining=6096)
[2026-06-08T09:10:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2477)
[2026-06-08T09:10:23] Filtering fusions with anchors <=23nt (remaining=1983)
[2026-06-08T09:10:24] Filtering end-to-end fusions with low support (remaining=1906)
[2026-06-08T09:10:25] Filtering fusions with no coverage around the breakpoints (remaining=1848)
[2026-06-08T09:10:25] Indexing gene sequences 
[2026-06-08T09:10:32] Filtering genes with >=30% identity (remaining=665)
[2026-06-08T09:10:36] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=405)
[2026-06-08T09:10:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=264)
[2026-06-08T09:10:42] Searching for additional isoforms (remaining=398)
[2026-06-08T09:10:44] Assigning confidence scores to events 
[2026-06-08T09:10:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:10:47] Writing fusions to file 'FFPE_HD789_01_RNA_13_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:10:51] Writing discarded fusions to file 'FFPE_HD789_01_RNA_13_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:11:22] Freeing resources
[2026-06-08T09:11:38] Done (elapsed time=00:12:18, CPU time=00:12:16, peak memory=14.4gb)