[2026-05-28T20:08:13] Launching Arriba 2.4.0
[2026-05-28T20:08:13] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:08:30] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:08:36] Reading chimeric alignments from 'A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=490704)
[2026-05-28T20:08:41] Marking multi-mapping alignments (marked=448112)
[2026-05-28T20:08:41] Detecting strandedness (no)
[2026-05-28T20:08:41] Annotating alignments 
[2026-05-28T20:08:43] Filtering duplicates (remaining=190382)
[2026-05-28T20:08:43] 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=162554)
[2026-05-28T20:08:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=162554)
[2026-05-28T20:08:44] Filtering viral contigs with expression lower than the top 5 (remaining=162554)
[2026-05-28T20:08:44] Filtering viral contigs with less than 5% coverage (remaining=162554)
[2026-05-28T20:08:44] Estimating fragment length (mate gap mean=-16.1034, mate gap stddev=2.01948, read length mean=50.3208)
[2026-05-28T20:08:44] Filtering read-through fragments with a distance <=10000bp (remaining=162472)
[2026-05-28T20:08:44] Filtering inconsistently clipped mates (remaining=157888)
[2026-05-28T20:08:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=149166)
[2026-05-28T20:08:45] Filtering fragments with small insert size (remaining=148421)
[2026-05-28T20:08:45] Filtering alignments with long gaps (remaining=148421)
[2026-05-28T20:08:45] Filtering fragments with both mates in the same gene (remaining=147967)
[2026-05-28T20:08:45] Filtering fusions arising from hairpin structures (remaining=144317)
[2026-05-28T20:08:45] Filtering reads with a mismatch p-value <=0.01 (remaining=2371)
[2026-05-28T20:08:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=523)
[2026-05-28T20:08:45] Finding fusions and counting supporting reads (total=535)
[2026-05-28T20:08:46] Merging adjacent fusion breakpoints (remaining=534)
[2026-05-28T20:08:46] Filtering multi-mapping fusions by alignment score and read support (remaining=512)
[2026-05-28T20:08:47] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:08:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=505)
[2026-05-28T20:08:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=505)
[2026-05-28T20:08:47] Filtering fusions with <2 supporting reads (remaining=26)
[2026-05-28T20:08:47] Filtering fusions with an e-value >=0.3 (remaining=26)
[2026-05-28T20:08:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=26)
[2026-05-28T20:08:48] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6)
[2026-05-28T20:08:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6)
[2026-05-28T20:08:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5)
[2026-05-28T20:08:48] Searching for fusions with spliced split reads (remaining=5)
[2026-05-28T20:08:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=5)
[2026-05-28T20:08:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5)
[2026-05-28T20:08:48] Searching for fusions with >=4 spliced events (remaining=5)
[2026-05-28T20:08:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5)
[2026-05-28T20:09:05] Filtering fusions with anchors <=23nt (remaining=0)
[2026-05-28T20:09:05] Filtering end-to-end fusions with low support (remaining=0)
[2026-05-28T20:09:05] Filtering fusions with no coverage around the breakpoints (remaining=0)
[2026-05-28T20:09:05] Indexing gene sequences 
[2026-05-28T20:09:05] Filtering genes with >=30% identity (remaining=0)
[2026-05-28T20:09:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:09:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:09:05] Searching for additional isoforms (remaining=0)
[2026-05-28T20:09:05] Assigning confidence scores to events 
[2026-05-28T20:09:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:09:06] Writing fusions to file 'A549_FFPE_01_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-05-28T20:09:06] Writing discarded fusions to file 'A549_FFPE_01_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-05-28T20:09:07] Freeing resources
[2026-05-28T20:09:08] Done (elapsed time=00:00:55, CPU time=00:00:54, peak memory=4.55gb)