[2026-05-28T21:28:10] Launching Arriba 2.4.0
[2026-05-28T21:28:10] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:28:25] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:28:29] Reading chimeric alignments from 'Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=11116312)
[2026-05-28T21:37:07] Marking multi-mapping alignments (marked=7190054)
[2026-05-28T21:37:13] Detecting strandedness (no)
[2026-05-28T21:37:13] Annotating alignments 
[2026-05-28T21:38:02] Filtering duplicates (remaining=8262193)
[2026-05-28T21:38:11] 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=7823534)
[2026-05-28T21:38:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7823534)
[2026-05-28T21:38:16] Filtering viral contigs with expression lower than the top 5 (remaining=7823534)
[2026-05-28T21:38:22] Filtering viral contigs with less than 5% coverage (remaining=7823534)
[2026-05-28T21:38:24] Estimating fragment length (mate gap mean=-82.7118, mate gap stddev=33.3597, read length mean=127.919)
[2026-05-28T21:38:25] Filtering read-through fragments with a distance <=10000bp (remaining=7443599)
[2026-05-28T21:38:27] Filtering inconsistently clipped mates (remaining=7320255)
[2026-05-28T21:38:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7045412)
[2026-05-28T21:38:36] Filtering fragments with small insert size (remaining=7044267)
[2026-05-28T21:38:38] Filtering alignments with long gaps (remaining=7044266)
[2026-05-28T21:38:41] Filtering fragments with both mates in the same gene (remaining=7042791)
[2026-05-28T21:38:43] Filtering fusions arising from hairpin structures (remaining=6561828)
[2026-05-28T21:38:46] Filtering reads with a mismatch p-value <=0.01 (remaining=3049325)
[2026-05-28T21:39:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1299230)
[2026-05-28T21:39:19] Finding fusions and counting supporting reads (total=1025092)
[2026-05-28T21:39:39] Merging adjacent fusion breakpoints (remaining=1016327)
[2026-05-28T21:39:42] Filtering multi-mapping fusions by alignment score and read support (remaining=647098)
[2026-05-28T21:40:21] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:40:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=644547)
[2026-05-28T21:40:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=394396)
[2026-05-28T21:40:35] Filtering fusions with <2 supporting reads (remaining=39309)
[2026-05-28T21:40:36] Filtering fusions with an e-value >=0.3 (remaining=8780)
[2026-05-28T21:40:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8824)
[2026-05-28T21:40:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8328)
[2026-05-28T21:40:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8329)
[2026-05-28T21:40:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7204)
[2026-05-28T21:40:52] Searching for fusions with spliced split reads (remaining=7228)
[2026-05-28T21:40:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=4562)
[2026-05-28T21:41:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4527)
[2026-05-28T21:41:02] Searching for fusions with >=4 spliced events (remaining=5864)
[2026-05-28T21:41:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2625)
[2026-05-28T21:41:22] Filtering fusions with anchors <=23nt (remaining=2189)
[2026-05-28T21:41:23] Filtering end-to-end fusions with low support (remaining=2128)
[2026-05-28T21:41:24] Filtering fusions with no coverage around the breakpoints (remaining=2101)
[2026-05-28T21:41:25] Indexing gene sequences 
[2026-05-28T21:41:37] Filtering genes with >=30% identity (remaining=777)
[2026-05-28T21:41:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=429)
[2026-05-28T21:42:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=285)
[2026-05-28T21:42:03] Searching for additional isoforms (remaining=471)
[2026-05-28T21:42:05] Assigning confidence scores to events 
[2026-05-28T21:42:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:42:11] Writing fusions to file 'Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:42:17] Writing discarded fusions to file 'Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:43:04] Freeing resources
[2026-05-28T21:43:27] Done (elapsed time=00:15:17, CPU time=00:15:16, peak memory=16.2gb)