[2026-06-08T07:23:23] Launching Arriba 2.4.0
[2026-06-08T07:23:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:23:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:23:42] Reading chimeric alignments from 'A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=436252)
[2026-06-08T07:23:48] Marking multi-mapping alignments (marked=398600)
[2026-06-08T07:23:48] Detecting strandedness (no)
[2026-06-08T07:23:48] Annotating alignments 
[2026-06-08T07:23:50] Filtering duplicates (remaining=178071)
[2026-06-08T07:23:50] 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=152813)
[2026-06-08T07:23:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=152813)
[2026-06-08T07:23:51] Filtering viral contigs with expression lower than the top 5 (remaining=152813)
[2026-06-08T07:23:51] Filtering viral contigs with less than 5% coverage (remaining=152813)
[2026-06-08T07:23:51] Estimating fragment length (mate gap mean=-16.3177, mate gap stddev=2.22878, read length mean=50.158)
[2026-06-08T07:23:51] Filtering read-through fragments with a distance <=10000bp (remaining=152749)
[2026-06-08T07:23:51] Filtering inconsistently clipped mates (remaining=147092)
[2026-06-08T07:23:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=139723)
[2026-06-08T07:23:52] Filtering fragments with small insert size (remaining=139081)
[2026-06-08T07:23:52] Filtering alignments with long gaps (remaining=139081)
[2026-06-08T07:23:52] Filtering fragments with both mates in the same gene (remaining=138519)
[2026-06-08T07:23:52] Filtering fusions arising from hairpin structures (remaining=134238)
[2026-06-08T07:23:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2547)
[2026-06-08T07:23:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=408)
[2026-06-08T07:23:52] Finding fusions and counting supporting reads (total=422)
[2026-06-08T07:23:53] Merging adjacent fusion breakpoints (remaining=422)
[2026-06-08T07:23:53] Filtering multi-mapping fusions by alignment score and read support (remaining=420)
[2026-06-08T07:23:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:23:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=409)
[2026-06-08T07:23:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=409)
[2026-06-08T07:23:54] Filtering fusions with <2 supporting reads (remaining=21)
[2026-06-08T07:23:54] Filtering fusions with an e-value >=0.3 (remaining=20)
[2026-06-08T07:23:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=20)
[2026-06-08T07:23:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4)
[2026-06-08T07:23:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4)
[2026-06-08T07:23:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4)
[2026-06-08T07:23:54] Searching for fusions with spliced split reads (remaining=4)
[2026-06-08T07:23:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=4)
[2026-06-08T07:23:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4)
[2026-06-08T07:23:55] Searching for fusions with >=4 spliced events (remaining=4)
[2026-06-08T07:23:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4)
[2026-06-08T07:24:10] Filtering fusions with anchors <=23nt (remaining=0)
[2026-06-08T07:24:10] Filtering end-to-end fusions with low support (remaining=0)
[2026-06-08T07:24:10] Filtering fusions with no coverage around the breakpoints (remaining=0)
[2026-06-08T07:24:10] Indexing gene sequences 
[2026-06-08T07:24:10] Filtering genes with >=30% identity (remaining=0)
[2026-06-08T07:24:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-08T07:24:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:24:10] Searching for additional isoforms (remaining=0)
[2026-06-08T07:24:10] Assigning confidence scores to events 
[2026-06-08T07:24:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:24:11] Writing fusions to file 'A549_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:24:11] Writing discarded fusions to file 'A549_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:24:11] Freeing resources
[2026-06-08T07:24:13] Done (elapsed time=00:00:50, CPU time=00:00:49, peak memory=4.49gb)