[2026-05-28T20:55:08] Launching Arriba 2.4.0
[2026-05-28T20:55:08] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:55:23] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:55:29] Reading chimeric alignments from 'BT-20_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=9410937)
[2026-05-28T20:59:26] Marking multi-mapping alignments (marked=7507334)
[2026-05-28T20:59:29] Detecting strandedness (reverse)
[2026-05-28T20:59:29] Assigning strands to alignments 
[2026-05-28T20:59:31] Annotating alignments 
[2026-05-28T21:00:07] Filtering duplicates (remaining=5069794)
[2026-05-28T21:00:13] 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=4587553)
[2026-05-28T21:00:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4587553)
[2026-05-28T21:00:17] Filtering viral contigs with expression lower than the top 5 (remaining=4587553)
[2026-05-28T21:00:21] Filtering viral contigs with less than 5% coverage (remaining=4587553)
[2026-05-28T21:00:23] Estimating fragment length (mate gap mean=-62.7588, mate gap stddev=30.5443, read length mean=94.9535)
[2026-05-28T21:00:23] Filtering read-through fragments with a distance <=10000bp (remaining=4509799)
[2026-05-28T21:00:25] Filtering inconsistently clipped mates (remaining=4376825)
[2026-05-28T21:00:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3784654)
[2026-05-28T21:00:30] Filtering fragments with small insert size (remaining=3778965)
[2026-05-28T21:00:32] Filtering alignments with long gaps (remaining=3778965)
[2026-05-28T21:00:34] Filtering fragments with both mates in the same gene (remaining=3777325)
[2026-05-28T21:00:36] Filtering fusions arising from hairpin structures (remaining=3548720)
[2026-05-28T21:00:38] Filtering reads with a mismatch p-value <=0.01 (remaining=741833)
[2026-05-28T21:00:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=359081)
[2026-05-28T21:00:50] Finding fusions and counting supporting reads (total=369587)
[2026-05-28T21:01:05] Merging adjacent fusion breakpoints (remaining=367939)
[2026-05-28T21:01:06] Filtering multi-mapping fusions by alignment score and read support (remaining=158649)
[2026-05-28T21:01:37] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:01:44] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=157175)
[2026-05-28T21:01:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=134078)
[2026-05-28T21:01:45] Filtering fusions with <2 supporting reads (remaining=4176)
[2026-05-28T21:01:46] Filtering fusions with an e-value >=0.3 (remaining=836)
[2026-05-28T21:01:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=866)
[2026-05-28T21:01:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=737)
[2026-05-28T21:01:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=737)
[2026-05-28T21:01:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=737)
[2026-05-28T21:01:56] Searching for fusions with spliced split reads (remaining=766)
[2026-05-28T21:02:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=638)
[2026-05-28T21:02:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=632)
[2026-05-28T21:02:03] Searching for fusions with >=4 spliced events (remaining=660)
[2026-05-28T21:02:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=172)
[2026-05-28T21:02:20] Filtering fusions with anchors <=23nt (remaining=145)
[2026-05-28T21:02:21] Filtering end-to-end fusions with low support (remaining=137)
[2026-05-28T21:02:22] Filtering fusions with no coverage around the breakpoints (remaining=132)
[2026-05-28T21:02:22] Indexing gene sequences 
[2026-05-28T21:02:24] Filtering genes with >=30% identity (remaining=56)
[2026-05-28T21:02:25] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=38)
[2026-05-28T21:02:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=35)
[2026-05-28T21:02:27] Searching for additional isoforms (remaining=40)
[2026-05-28T21:02:29] Assigning confidence scores to events 
[2026-05-28T21:02:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:02:33] Writing fusions to file 'BT-20_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T21:02:33] Writing discarded fusions to file 'BT-20_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T21:03:09] Freeing resources
[2026-05-28T21:03:26] Done (elapsed time=00:08:18, CPU time=00:08:18, peak memory=14.3gb)