[2026-05-28T20:11:13] Launching Arriba 2.4.0
[2026-05-28T20:11:13] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:11:29] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:11:34] Reading chimeric alignments from '22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=1934542)
[2026-05-28T20:12:14] Marking multi-mapping alignments (marked=1588768)
[2026-05-28T20:12:15] Detecting strandedness (no)
[2026-05-28T20:12:16] Annotating alignments 
[2026-05-28T20:12:27] Filtering duplicates (remaining=952024)
[2026-05-28T20:12:29] 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=794561)
[2026-05-28T20:12:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=794561)
[2026-05-28T20:12:30] Filtering viral contigs with expression lower than the top 5 (remaining=794561)
[2026-05-28T20:12:31] Filtering viral contigs with less than 5% coverage (remaining=794561)
[2026-05-28T20:12:32] Estimating fragment length (mate gap mean=-53.1772, mate gap stddev=33.3547, read length mean=85.1571)
[2026-05-28T20:12:32] Filtering read-through fragments with a distance <=10000bp (remaining=782785)
[2026-05-28T20:12:33] Filtering inconsistently clipped mates (remaining=763077)
[2026-05-28T20:12:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=705109)
[2026-05-28T20:12:34] Filtering fragments with small insert size (remaining=704417)
[2026-05-28T20:12:35] Filtering alignments with long gaps (remaining=704417)
[2026-05-28T20:12:35] Filtering fragments with both mates in the same gene (remaining=703620)
[2026-05-28T20:12:36] Filtering fusions arising from hairpin structures (remaining=668691)
[2026-05-28T20:12:36] Filtering reads with a mismatch p-value <=0.01 (remaining=89787)
[2026-05-28T20:12:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=33163)
[2026-05-28T20:12:40] Finding fusions and counting supporting reads (total=34897)
[2026-05-28T20:12:43] Merging adjacent fusion breakpoints (remaining=34670)
[2026-05-28T20:12:44] Filtering multi-mapping fusions by alignment score and read support (remaining=17695)
[2026-05-28T20:12:53] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:12:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=17448)
[2026-05-28T20:12:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=13680)
[2026-05-28T20:12:54] Filtering fusions with <2 supporting reads (remaining=350)
[2026-05-28T20:12:54] Filtering fusions with an e-value >=0.3 (remaining=165)
[2026-05-28T20:12:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=167)
[2026-05-28T20:12:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=145)
[2026-05-28T20:12:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=145)
[2026-05-28T20:12:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=121)
[2026-05-28T20:12:57] Searching for fusions with spliced split reads (remaining=126)
[2026-05-28T20:12:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=110)
[2026-05-28T20:12:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=110)
[2026-05-28T20:12:59] Searching for fusions with >=4 spliced events (remaining=114)
[2026-05-28T20:12:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=23)
[2026-05-28T20:13:23] Filtering fusions with anchors <=23nt (remaining=7)
[2026-05-28T20:13:24] Filtering end-to-end fusions with low support (remaining=6)
[2026-05-28T20:13:24] Filtering fusions with no coverage around the breakpoints (remaining=6)
[2026-05-28T20:13:24] Indexing gene sequences 
[2026-05-28T20:13:24] Filtering genes with >=30% identity (remaining=3)
[2026-05-28T20:13:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:13:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:13:25] Searching for additional isoforms (remaining=0)
[2026-05-28T20:13:25] Assigning confidence scores to events 
[2026-05-28T20:13:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:13:26] Writing fusions to file '22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-05-28T20:13:26] Writing discarded fusions to file '22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-05-28T20:13:33] Freeing resources
[2026-05-28T20:13:39] Done (elapsed time=00:02:26, CPU time=00:02:25, peak memory=6.13gb)