[2026-05-28T20:09:29] Launching Arriba 2.4.0
[2026-05-28T20:09:29] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:09:44] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:09:50] Reading chimeric alignments from '22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=1716266)
[2026-05-28T20:10:35] Marking multi-mapping alignments (marked=1394708)
[2026-05-28T20:10:36] Detecting strandedness (no)
[2026-05-28T20:10:36] Annotating alignments 
[2026-05-28T20:10:43] Filtering duplicates (remaining=860578)
[2026-05-28T20:10:45] 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=711569)
[2026-05-28T20:10:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=711569)
[2026-05-28T20:10:45] Filtering viral contigs with expression lower than the top 5 (remaining=711569)
[2026-05-28T20:10:46] Filtering viral contigs with less than 5% coverage (remaining=711569)
[2026-05-28T20:10:46] Estimating fragment length (mate gap mean=-57.9999, mate gap stddev=34.1801, read length mean=90.4603)
[2026-05-28T20:10:46] Filtering read-through fragments with a distance <=10000bp (remaining=699509)
[2026-05-28T20:10:47] Filtering inconsistently clipped mates (remaining=681190)
[2026-05-28T20:10:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=629343)
[2026-05-28T20:10:48] Filtering fragments with small insert size (remaining=628667)
[2026-05-28T20:10:48] Filtering alignments with long gaps (remaining=628667)
[2026-05-28T20:10:48] Filtering fragments with both mates in the same gene (remaining=628117)
[2026-05-28T20:10:48] Filtering fusions arising from hairpin structures (remaining=593266)
[2026-05-28T20:10:49] Filtering reads with a mismatch p-value <=0.01 (remaining=86076)
[2026-05-28T20:10:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=33652)
[2026-05-28T20:10:51] Finding fusions and counting supporting reads (total=35484)
[2026-05-28T20:10:54] Merging adjacent fusion breakpoints (remaining=35276)
[2026-05-28T20:10:54] Filtering multi-mapping fusions by alignment score and read support (remaining=17688)
[2026-05-28T20:11:00] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:11:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=17399)
[2026-05-28T20:11:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=13521)
[2026-05-28T20:11:01] Filtering fusions with <2 supporting reads (remaining=315)
[2026-05-28T20:11:01] Filtering fusions with an e-value >=0.3 (remaining=137)
[2026-05-28T20:11:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=143)
[2026-05-28T20:11:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=116)
[2026-05-28T20:11:01] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=116)
[2026-05-28T20:11:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=103)
[2026-05-28T20:11:02] Searching for fusions with spliced split reads (remaining=104)
[2026-05-28T20:11:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=96)
[2026-05-28T20:11:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=96)
[2026-05-28T20:11:03] Searching for fusions with >=4 spliced events (remaining=96)
[2026-05-28T20:11:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=18)
[2026-05-28T20:11:27] Filtering fusions with anchors <=23nt (remaining=8)
[2026-05-28T20:11:28] Filtering end-to-end fusions with low support (remaining=7)
[2026-05-28T20:11:28] Filtering fusions with no coverage around the breakpoints (remaining=7)
[2026-05-28T20:11:28] Indexing gene sequences 
[2026-05-28T20:11:28] Filtering genes with >=30% identity (remaining=5)
[2026-05-28T20:11:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-05-28T20:11:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-05-28T20:11:29] Searching for additional isoforms (remaining=1)
[2026-05-28T20:11:29] Assigning confidence scores to events 
[2026-05-28T20:11:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:11:31] Writing fusions to file '22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T20:11:31] Writing discarded fusions to file '22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T20:11:38] Freeing resources
[2026-05-28T20:11:43] Done (elapsed time=00:02:14, CPU time=00:02:13, peak memory=5.92gb)