[2026-05-28T21:46:42] Launching Arriba 2.4.0
[2026-05-28T21:46:42] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:46:56] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:47:02] Reading chimeric alignments from 'FFPE_HD789_01_RNA_0004_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=8965634)
[2026-05-28T21:56:48] Marking multi-mapping alignments (marked=5658559)
[2026-05-28T21:56:52] Detecting strandedness (reverse)
[2026-05-28T21:56:52] Assigning strands to alignments 
[2026-05-28T21:56:53] Annotating alignments 
[2026-05-28T21:57:23] Filtering duplicates (remaining=6110735)
[2026-05-28T21:57:31] 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=5885647)
[2026-05-28T21:57:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5885647)
[2026-05-28T21:57:34] Filtering viral contigs with expression lower than the top 5 (remaining=5885647)
[2026-05-28T21:57:38] Filtering viral contigs with less than 5% coverage (remaining=5885647)
[2026-05-28T21:57:40] Estimating fragment length (mate gap mean=-83.9372, mate gap stddev=32.0682, read length mean=135.89)
[2026-05-28T21:57:41] Filtering read-through fragments with a distance <=10000bp (remaining=5641014)
[2026-05-28T21:57:42] Filtering inconsistently clipped mates (remaining=5553630)
[2026-05-28T21:57:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5280878)
[2026-05-28T21:57:48] Filtering fragments with small insert size (remaining=5280387)
[2026-05-28T21:57:50] Filtering alignments with long gaps (remaining=5280387)
[2026-05-28T21:57:52] Filtering fragments with both mates in the same gene (remaining=5279231)
[2026-05-28T21:57:54] Filtering fusions arising from hairpin structures (remaining=4976500)
[2026-05-28T21:57:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2556813)
[2026-05-28T21:58:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=916705)
[2026-05-28T21:58:19] Finding fusions and counting supporting reads (total=645573)
[2026-05-28T21:58:34] Merging adjacent fusion breakpoints (remaining=640665)
[2026-05-28T21:58:36] Filtering multi-mapping fusions by alignment score and read support (remaining=421116)
[2026-05-28T21:59:07] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:59:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=417458)
[2026-05-28T21:59:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=232542)
[2026-05-28T21:59:18] Filtering fusions with <2 supporting reads (remaining=36275)
[2026-05-28T21:59:19] Filtering fusions with an e-value >=0.3 (remaining=13159)
[2026-05-28T21:59:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13216)
[2026-05-28T21:59:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13157)
[2026-05-28T21:59:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13163)
[2026-05-28T21:59:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8179)
[2026-05-28T21:59:34] Searching for fusions with spliced split reads (remaining=8224)
[2026-05-28T21:59:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=4534)
[2026-05-28T21:59:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4488)
[2026-05-28T21:59:44] Searching for fusions with >=4 spliced events (remaining=5520)
[2026-05-28T21:59:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2196)
[2026-05-28T22:00:12] Filtering fusions with anchors <=23nt (remaining=1771)
[2026-05-28T22:00:13] Filtering end-to-end fusions with low support (remaining=1736)
[2026-05-28T22:00:14] Filtering fusions with no coverage around the breakpoints (remaining=1705)
[2026-05-28T22:00:14] Indexing gene sequences 
[2026-05-28T22:00:28] Filtering genes with >=30% identity (remaining=609)
[2026-05-28T22:00:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=341)
[2026-05-28T22:00:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=223)
[2026-05-28T22:00:38] Searching for additional isoforms (remaining=323)
[2026-05-28T22:00:40] Assigning confidence scores to events 
[2026-05-28T22:00:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T22:00:45] Writing fusions to file 'FFPE_HD789_01_RNA_0004_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T22:00:50] Writing discarded fusions to file 'FFPE_HD789_01_RNA_0004_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T22:01:38] Freeing resources
[2026-05-28T22:02:11] Done (elapsed time=00:15:29, CPU time=00:15:29, peak memory=13.5gb)