[2026-05-28T21:25:50] Launching Arriba 2.4.0
[2026-05-28T21:25:50] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:26:05] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:26:10] Reading chimeric alignments from 'SW780_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=11630680)
[2026-05-28T21:38:38] Marking multi-mapping alignments (marked=7852190)
[2026-05-28T21:38:45] Detecting strandedness (reverse)
[2026-05-28T21:38:45] Assigning strands to alignments 
[2026-05-28T21:38:49] Annotating alignments 
[2026-05-28T21:39:53] Filtering duplicates (remaining=8209200)
[2026-05-28T21:40:10] 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=7654987)
[2026-05-28T21:40:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7654987)
[2026-05-28T21:40:16] Filtering viral contigs with expression lower than the top 5 (remaining=7654987)
[2026-05-28T21:40:23] Filtering viral contigs with less than 5% coverage (remaining=7654987)
[2026-05-28T21:40:27] Estimating fragment length (mate gap mean=-84.8159, mate gap stddev=30.1818, read length mean=129.203)
[2026-05-28T21:40:27] Filtering read-through fragments with a distance <=10000bp (remaining=7289616)
[2026-05-28T21:40:30] Filtering inconsistently clipped mates (remaining=7156550)
[2026-05-28T21:40:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6804291)
[2026-05-28T21:40:40] Filtering fragments with small insert size (remaining=6803041)
[2026-05-28T21:40:43] Filtering alignments with long gaps (remaining=6803041)
[2026-05-28T21:40:47] Filtering fragments with both mates in the same gene (remaining=6801499)
[2026-05-28T21:40:51] Filtering fusions arising from hairpin structures (remaining=6358510)
[2026-05-28T21:40:56] Filtering reads with a mismatch p-value <=0.01 (remaining=3036590)
[2026-05-28T21:41:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=1259497)
[2026-05-28T21:41:38] Finding fusions and counting supporting reads (total=993364)
[2026-05-28T21:42:09] Merging adjacent fusion breakpoints (remaining=986984)
[2026-05-28T21:42:12] Filtering multi-mapping fusions by alignment score and read support (remaining=591133)
[2026-05-28T21:43:12] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:43:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=588749)
[2026-05-28T21:43:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=377773)
[2026-05-28T21:43:33] Filtering fusions with <2 supporting reads (remaining=35973)
[2026-05-28T21:43:34] Filtering fusions with an e-value >=0.3 (remaining=7982)
[2026-05-28T21:43:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8033)
[2026-05-28T21:43:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7829)
[2026-05-28T21:43:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7833)
[2026-05-28T21:43:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6536)
[2026-05-28T21:43:59] Searching for fusions with spliced split reads (remaining=6676)
[2026-05-28T21:44:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=4396)
[2026-05-28T21:44:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4357)
[2026-05-28T21:44:13] Searching for fusions with >=4 spliced events (remaining=5401)
[2026-05-28T21:44:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2486)
[2026-05-28T21:44:44] Filtering fusions with anchors <=23nt (remaining=2017)
[2026-05-28T21:44:45] Filtering end-to-end fusions with low support (remaining=1976)
[2026-05-28T21:44:47] Filtering fusions with no coverage around the breakpoints (remaining=1934)
[2026-05-28T21:44:48] Indexing gene sequences 
[2026-05-28T21:45:15] Filtering genes with >=30% identity (remaining=693)
[2026-05-28T21:45:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=395)
[2026-05-28T21:45:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=282)
[2026-05-28T21:45:39] Searching for additional isoforms (remaining=440)
[2026-05-28T21:45:41] Assigning confidence scores to events 
[2026-05-28T21:45:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:45:51] Writing fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T21:45:59] Writing discarded fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T21:47:18] Freeing resources
[2026-05-28T21:48:03] Done (elapsed time=00:22:13, CPU time=00:22:11, peak memory=16.6gb)