[2026-05-28T21:27:45] Launching Arriba 2.4.0
[2026-05-28T21:27:45] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:27:59] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:28:04] Reading chimeric alignments from 'FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=10901730)
[2026-05-28T21:36:34] Marking multi-mapping alignments (marked=6954530)
[2026-05-28T21:36:39] Detecting strandedness (reverse)
[2026-05-28T21:36:39] Assigning strands to alignments 
[2026-05-28T21:36:41] Annotating alignments 
[2026-05-28T21:37:16] Filtering duplicates (remaining=6369501)
[2026-05-28T21:37:23] 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=6090071)
[2026-05-28T21:37:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6090071)
[2026-05-28T21:37:28] Filtering viral contigs with expression lower than the top 5 (remaining=6090071)
[2026-05-28T21:37:32] Filtering viral contigs with less than 5% coverage (remaining=6090071)
[2026-05-28T21:37:35] Estimating fragment length (mate gap mean=-85.1032, mate gap stddev=31.842, read length mean=131.381)
[2026-05-28T21:37:35] Filtering read-through fragments with a distance <=10000bp (remaining=5841934)
[2026-05-28T21:37:37] Filtering inconsistently clipped mates (remaining=5740158)
[2026-05-28T21:37:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5499294)
[2026-05-28T21:37:43] Filtering fragments with small insert size (remaining=5498565)
[2026-05-28T21:37:45] Filtering alignments with long gaps (remaining=5498564)
[2026-05-28T21:37:47] Filtering fragments with both mates in the same gene (remaining=5497615)
[2026-05-28T21:37:49] Filtering fusions arising from hairpin structures (remaining=5199625)
[2026-05-28T21:37:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2466010)
[2026-05-28T21:38:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=910626)
[2026-05-28T21:38:19] Finding fusions and counting supporting reads (total=648241)
[2026-05-28T21:38:36] Merging adjacent fusion breakpoints (remaining=640724)
[2026-05-28T21:38:38] Filtering multi-mapping fusions by alignment score and read support (remaining=401520)
[2026-05-28T21:39:11] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:39:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=399413)
[2026-05-28T21:39:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=215720)
[2026-05-28T21:39:19] Filtering fusions with <2 supporting reads (remaining=30895)
[2026-05-28T21:39:19] Filtering fusions with an e-value >=0.3 (remaining=9704)
[2026-05-28T21:39:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9747)
[2026-05-28T21:39:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9677)
[2026-05-28T21:39:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9701)
[2026-05-28T21:39:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7301)
[2026-05-28T21:39:31] Searching for fusions with spliced split reads (remaining=7396)
[2026-05-28T21:39:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=4182)
[2026-05-28T21:39:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4141)
[2026-05-28T21:39:38] Searching for fusions with >=4 spliced events (remaining=4999)
[2026-05-28T21:39:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2035)
[2026-05-28T21:39:59] Filtering fusions with anchors <=23nt (remaining=1468)
[2026-05-28T21:39:59] Filtering end-to-end fusions with low support (remaining=1425)
[2026-05-28T21:40:00] Filtering fusions with no coverage around the breakpoints (remaining=1402)
[2026-05-28T21:40:01] Indexing gene sequences 
[2026-05-28T21:40:07] Filtering genes with >=30% identity (remaining=375)
[2026-05-28T21:40:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=104)
[2026-05-28T21:40:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=97)
[2026-05-28T21:40:13] Searching for additional isoforms (remaining=123)
[2026-05-28T21:40:15] Assigning confidence scores to events 
[2026-05-28T21:40:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:40:18] Writing fusions to file 'FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T21:40:19] Writing discarded fusions to file 'FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T21:40:47] Freeing resources
[2026-05-28T21:41:06] Done (elapsed time=00:13:21, CPU time=00:13:20, peak memory=15.3gb)