[2026-06-08T08:34:06] Launching Arriba 2.4.0
[2026-06-08T08:34:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:21] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:25] Reading chimeric alignments from 'SW780_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=11630680)
[2026-06-08T08:42:53] Marking multi-mapping alignments (marked=7852190)
[2026-06-08T08:42:58] Detecting strandedness (reverse)
[2026-06-08T08:42:58] Assigning strands to alignments 
[2026-06-08T08:43:00] Annotating alignments 
[2026-06-08T08:43:37] Filtering duplicates (remaining=8209200)
[2026-06-08T08:43:45] 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=7654987)
[2026-06-08T08:43:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7654987)
[2026-06-08T08:43:50] Filtering viral contigs with expression lower than the top 5 (remaining=7654987)
[2026-06-08T08:43:54] Filtering viral contigs with less than 5% coverage (remaining=7654987)
[2026-06-08T08:43:57] Estimating fragment length (mate gap mean=-84.8159, mate gap stddev=30.1818, read length mean=129.203)
[2026-06-08T08:43:57] Filtering read-through fragments with a distance <=10000bp (remaining=7289616)
[2026-06-08T08:43:59] Filtering inconsistently clipped mates (remaining=7156550)
[2026-06-08T08:44:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6804291)
[2026-06-08T08:44:07] Filtering fragments with small insert size (remaining=6803041)
[2026-06-08T08:44:09] Filtering alignments with long gaps (remaining=6803041)
[2026-06-08T08:44:11] Filtering fragments with both mates in the same gene (remaining=6801499)
[2026-06-08T08:44:14] Filtering fusions arising from hairpin structures (remaining=6358510)
[2026-06-08T08:44:16] Filtering reads with a mismatch p-value <=0.01 (remaining=3036590)
[2026-06-08T08:44:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=1259497)
[2026-06-08T08:44:47] Finding fusions and counting supporting reads (total=993364)
[2026-06-08T08:45:06] Merging adjacent fusion breakpoints (remaining=986984)
[2026-06-08T08:45:08] Filtering multi-mapping fusions by alignment score and read support (remaining=591133)
[2026-06-08T08:45:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=588749)
[2026-06-08T08:45:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=377773)
[2026-06-08T08:45:55] Filtering fusions with <2 supporting reads (remaining=35973)
[2026-06-08T08:45:56] Filtering fusions with an e-value >=0.3 (remaining=7982)
[2026-06-08T08:45:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8033)
[2026-06-08T08:46:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7829)
[2026-06-08T08:46:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7833)
[2026-06-08T08:46:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6536)
[2026-06-08T08:46:10] Searching for fusions with spliced split reads (remaining=6676)
[2026-06-08T08:46:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=4396)
[2026-06-08T08:46:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4357)
[2026-06-08T08:46:18] Searching for fusions with >=4 spliced events (remaining=5401)
[2026-06-08T08:46:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2486)
[2026-06-08T08:46:37] Filtering fusions with anchors <=23nt (remaining=2017)
[2026-06-08T08:46:38] Filtering end-to-end fusions with low support (remaining=1976)
[2026-06-08T08:46:39] Filtering fusions with no coverage around the breakpoints (remaining=1934)
[2026-06-08T08:46:39] Indexing gene sequences 
[2026-06-08T08:46:48] Filtering genes with >=30% identity (remaining=693)
[2026-06-08T08:46:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=395)
[2026-06-08T08:47:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=282)
[2026-06-08T08:47:03] Searching for additional isoforms (remaining=440)
[2026-06-08T08:47:05] Assigning confidence scores to events 
[2026-06-08T08:47:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:09] Writing fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:47:14] Writing discarded fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:52] Freeing resources
[2026-06-08T08:48:11] Done (elapsed time=00:14:05, CPU time=00:14:04, peak memory=16.6gb)