[2026-06-08T07:27:22] Launching Arriba 2.4.0
[2026-06-08T07:27:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:27:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:27:47] Reading chimeric alignments from '22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=2300751)
[2026-06-08T07:28:41] Marking multi-mapping alignments (marked=1913294)
[2026-06-08T07:28:42] Detecting strandedness (reverse)
[2026-06-08T07:28:42] Assigning strands to alignments 
[2026-06-08T07:28:43] Annotating alignments 
[2026-06-08T07:28:54] Filtering duplicates (remaining=1094778)
[2026-06-08T07:28:56] 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=894404)
[2026-06-08T07:28:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=894404)
[2026-06-08T07:28:57] Filtering viral contigs with expression lower than the top 5 (remaining=894404)
[2026-06-08T07:28:58] Filtering viral contigs with less than 5% coverage (remaining=894404)
[2026-06-08T07:28:59] Estimating fragment length (mate gap mean=-54.1752, mate gap stddev=34.5644, read length mean=84.8091)
[2026-06-08T07:28:59] Filtering read-through fragments with a distance <=10000bp (remaining=881680)
[2026-06-08T07:29:00] Filtering inconsistently clipped mates (remaining=859388)
[2026-06-08T07:29:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=793407)
[2026-06-08T07:29:01] Filtering fragments with small insert size (remaining=792462)
[2026-06-08T07:29:02] Filtering alignments with long gaps (remaining=792462)
[2026-06-08T07:29:02] Filtering fragments with both mates in the same gene (remaining=791586)
[2026-06-08T07:29:03] Filtering fusions arising from hairpin structures (remaining=750806)
[2026-06-08T07:29:04] Filtering reads with a mismatch p-value <=0.01 (remaining=92189)
[2026-06-08T07:29:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=36228)
[2026-06-08T07:29:07] Finding fusions and counting supporting reads (total=38069)
[2026-06-08T07:29:12] Merging adjacent fusion breakpoints (remaining=37805)
[2026-06-08T07:29:13] Filtering multi-mapping fusions by alignment score and read support (remaining=19062)
[2026-06-08T07:29:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:29:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=18746)
[2026-06-08T07:29:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=14855)
[2026-06-08T07:29:25] Filtering fusions with <2 supporting reads (remaining=302)
[2026-06-08T07:29:25] Filtering fusions with an e-value >=0.3 (remaining=121)
[2026-06-08T07:29:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=125)
[2026-06-08T07:29:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=101)
[2026-06-08T07:29:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=101)
[2026-06-08T07:29:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=88)
[2026-06-08T07:29:29] Searching for fusions with spliced split reads (remaining=89)
[2026-06-08T07:29:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=79)
[2026-06-08T07:29:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=79)
[2026-06-08T07:29:31] Searching for fusions with >=4 spliced events (remaining=79)
[2026-06-08T07:29:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17)
[2026-06-08T07:29:51] Filtering fusions with anchors <=23nt (remaining=5)
[2026-06-08T07:29:51] Filtering end-to-end fusions with low support (remaining=5)
[2026-06-08T07:29:52] Filtering fusions with no coverage around the breakpoints (remaining=5)
[2026-06-08T07:29:52] Indexing gene sequences 
[2026-06-08T07:29:52] Filtering genes with >=30% identity (remaining=1)
[2026-06-08T07:29:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-08T07:29:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:29:53] Searching for additional isoforms (remaining=0)
[2026-06-08T07:29:53] Assigning confidence scores to events 
[2026-06-08T07:29:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:29:55] Writing fusions to file '22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:29:55] Writing discarded fusions to file '22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:30:05] Freeing resources
[2026-06-08T07:30:12] Done (elapsed time=00:02:50, CPU time=00:02:48, peak memory=6.5gb)