[2026-05-28T21:44:45] Launching Arriba 2.4.0
[2026-05-28T21:44:45] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:44:58] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:45:02] Reading chimeric alignments from 'FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=12178660)
[2026-05-28T21:54:25] Marking multi-mapping alignments (marked=8315155)
[2026-05-28T21:54:30] Detecting strandedness (reverse)
[2026-05-28T21:54:30] Assigning strands to alignments 
[2026-05-28T21:54:33] Annotating alignments 
[2026-05-28T21:55:20] Filtering duplicates (remaining=8085264)
[2026-05-28T21:55:31] 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=7433638)
[2026-05-28T21:55:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7433638)
[2026-05-28T21:55:36] Filtering viral contigs with expression lower than the top 5 (remaining=7433638)
[2026-05-28T21:55:42] Filtering viral contigs with less than 5% coverage (remaining=7433638)
[2026-05-28T21:55:45] Estimating fragment length (mate gap mean=-85.4397, mate gap stddev=31.9276, read length mean=131.808)
[2026-05-28T21:55:45] Filtering read-through fragments with a distance <=10000bp (remaining=7167767)
[2026-05-28T21:55:48] Filtering inconsistently clipped mates (remaining=7070869)
[2026-05-28T21:55:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6770650)
[2026-05-28T21:55:56] Filtering fragments with small insert size (remaining=6769684)
[2026-05-28T21:55:58] Filtering alignments with long gaps (remaining=6769684)
[2026-05-28T21:56:01] Filtering fragments with both mates in the same gene (remaining=6767999)
[2026-05-28T21:56:04] Filtering fusions arising from hairpin structures (remaining=6378726)
[2026-05-28T21:56:07] Filtering reads with a mismatch p-value <=0.01 (remaining=2884741)
[2026-05-28T21:56:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=985143)
[2026-05-28T21:56:36] Finding fusions and counting supporting reads (total=768910)
[2026-05-28T21:57:01] Merging adjacent fusion breakpoints (remaining=763542)
[2026-05-28T21:57:04] Filtering multi-mapping fusions by alignment score and read support (remaining=487314)
[2026-05-28T21:57:49] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:58:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=483816)
[2026-05-28T21:58:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=289903)
[2026-05-28T21:58:05] Filtering fusions with <2 supporting reads (remaining=33417)
[2026-05-28T21:58:06] Filtering fusions with an e-value >=0.3 (remaining=9434)
[2026-05-28T21:58:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9485)
[2026-05-28T21:58:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9353)
[2026-05-28T21:58:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9359)
[2026-05-28T21:58:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6506)
[2026-05-28T21:58:23] Searching for fusions with spliced split reads (remaining=6519)
[2026-05-28T21:58:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=4031)
[2026-05-28T21:58:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3995)
[2026-05-28T21:58:34] Searching for fusions with >=4 spliced events (remaining=4841)
[2026-05-28T21:58:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2030)
[2026-05-28T21:58:56] Filtering fusions with anchors <=23nt (remaining=1529)
[2026-05-28T21:58:57] Filtering end-to-end fusions with low support (remaining=1482)
[2026-05-28T21:58:59] Filtering fusions with no coverage around the breakpoints (remaining=1467)
[2026-05-28T21:59:00] Indexing gene sequences 
[2026-05-28T21:59:10] Filtering genes with >=30% identity (remaining=564)
[2026-05-28T21:59:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=337)
[2026-05-28T21:59:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=229)
[2026-05-28T21:59:21] Searching for additional isoforms (remaining=340)
[2026-05-28T21:59:23] Assigning confidence scores to events 
[2026-05-28T21:59:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:59:29] Writing fusions to file 'FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:59:33] Writing discarded fusions to file 'FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T22:00:23] Freeing resources
[2026-05-28T22:00:50] Done (elapsed time=00:16:05, CPU time=00:16:05, peak memory=17.1gb)