[2026-05-28T20:07:46] Launching Arriba 2.4.0
[2026-05-28T20:07:46] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:08:04] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:08:10] Reading chimeric alignments from 'A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=195408)
[2026-05-28T20:08:13] Marking multi-mapping alignments (marked=178144)
[2026-05-28T20:08:13] Detecting strandedness (no)
[2026-05-28T20:08:13] Annotating alignments 
[2026-05-28T20:08:15] Filtering duplicates (remaining=89789)
[2026-05-28T20:08:15] 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=77696)
[2026-05-28T20:08:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=77696)
[2026-05-28T20:08:15] Filtering viral contigs with expression lower than the top 5 (remaining=77696)
[2026-05-28T20:08:15] Filtering viral contigs with less than 5% coverage (remaining=77696)
[2026-05-28T20:08:15] Estimating fragment length (mate gap mean=-16.3659, mate gap stddev=2.25761, read length mean=51.5914)
[2026-05-28T20:08:15] Filtering read-through fragments with a distance <=10000bp (remaining=77674)
[2026-05-28T20:08:15] Filtering inconsistently clipped mates (remaining=74426)
[2026-05-28T20:08:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=71262)
[2026-05-28T20:08:15] Filtering fragments with small insert size (remaining=70900)
[2026-05-28T20:08:16] Filtering alignments with long gaps (remaining=70900)
[2026-05-28T20:08:16] Filtering fragments with both mates in the same gene (remaining=70554)
[2026-05-28T20:08:16] Filtering fusions arising from hairpin structures (remaining=67842)
[2026-05-28T20:08:16] Filtering reads with a mismatch p-value <=0.01 (remaining=1374)
[2026-05-28T20:08:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=223)
[2026-05-28T20:08:16] Finding fusions and counting supporting reads (total=224)
[2026-05-28T20:08:16] Merging adjacent fusion breakpoints (remaining=224)
[2026-05-28T20:08:16] Filtering multi-mapping fusions by alignment score and read support (remaining=220)
[2026-05-28T20:08:17] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:08:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=219)
[2026-05-28T20:08:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=219)
[2026-05-28T20:08:17] Filtering fusions with <2 supporting reads (remaining=11)
[2026-05-28T20:08:17] Filtering fusions with an e-value >=0.3 (remaining=11)
[2026-05-28T20:08:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11)
[2026-05-28T20:08:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2)
[2026-05-28T20:08:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2)
[2026-05-28T20:08:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1)
[2026-05-28T20:08:17] Searching for fusions with spliced split reads (remaining=1)
[2026-05-28T20:08:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-05-28T20:08:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1)
[2026-05-28T20:08:17] Searching for fusions with >=4 spliced events (remaining=1)
[2026-05-28T20:08:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1)
[2026-05-28T20:08:34] Filtering fusions with anchors <=23nt (remaining=0)
[2026-05-28T20:08:34] Filtering end-to-end fusions with low support (remaining=0)
[2026-05-28T20:08:34] Filtering fusions with no coverage around the breakpoints (remaining=0)
[2026-05-28T20:08:34] Indexing gene sequences 
[2026-05-28T20:08:34] Filtering genes with >=30% identity (remaining=0)
[2026-05-28T20:08:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:08:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:08:34] Searching for additional isoforms (remaining=0)
[2026-05-28T20:08:34] Assigning confidence scores to events 
[2026-05-28T20:08:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:08:35] Writing fusions to file 'A549_FFPE_01_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T20:08:35] Writing discarded fusions to file 'A549_FFPE_01_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T20:08:35] Freeing resources
[2026-05-28T20:08:37] Done (elapsed time=00:00:51, CPU time=00:00:50, peak memory=4.27gb)