[2026-06-08T08:41:29] Launching Arriba 2.4.0
[2026-06-08T08:41:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:42] Reading chimeric alignments from 'FFPE_HD789_01_RNA_13_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9664354)
[2026-06-08T08:48:38] Marking multi-mapping alignments (marked=6342330)
[2026-06-08T08:48:42] Detecting strandedness (reverse)
[2026-06-08T08:48:42] Assigning strands to alignments 
[2026-06-08T08:48:44] Annotating alignments 
[2026-06-08T08:49:14] Filtering duplicates (remaining=6842695)
[2026-06-08T08:49:20] 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=6436283)
[2026-06-08T08:49:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6436283)
[2026-06-08T08:49:24] Filtering viral contigs with expression lower than the top 5 (remaining=6436283)
[2026-06-08T08:49:29] Filtering viral contigs with less than 5% coverage (remaining=6436283)
[2026-06-08T08:49:31] Estimating fragment length (mate gap mean=-82.8681, mate gap stddev=33.0713, read length mean=136.735)
[2026-06-08T08:49:31] Filtering read-through fragments with a distance <=10000bp (remaining=6162875)
[2026-06-08T08:49:33] Filtering inconsistently clipped mates (remaining=6074191)
[2026-06-08T08:49:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5870904)
[2026-06-08T08:49:39] Filtering fragments with small insert size (remaining=5870347)
[2026-06-08T08:49:41] Filtering alignments with long gaps (remaining=5870346)
[2026-06-08T08:49:43] Filtering fragments with both mates in the same gene (remaining=5869146)
[2026-06-08T08:49:45] Filtering fusions arising from hairpin structures (remaining=5511711)
[2026-06-08T08:49:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2609099)
[2026-06-08T08:50:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=1042143)
[2026-06-08T08:50:13] Finding fusions and counting supporting reads (total=784474)
[2026-06-08T08:50:28] Merging adjacent fusion breakpoints (remaining=779827)
[2026-06-08T08:50:30] Filtering multi-mapping fusions by alignment score and read support (remaining=511822)
[2026-06-08T08:51:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=507519)
[2026-06-08T08:51:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=316137)
[2026-06-08T08:51:09] Filtering fusions with <2 supporting reads (remaining=42488)
[2026-06-08T08:51:10] Filtering fusions with an e-value >=0.3 (remaining=15379)
[2026-06-08T08:51:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=15435)
[2026-06-08T08:51:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=15374)
[2026-06-08T08:51:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15384)
[2026-06-08T08:51:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9412)
[2026-06-08T08:51:22] Searching for fusions with spliced split reads (remaining=9448)
[2026-06-08T08:51:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=4859)
[2026-06-08T08:51:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4819)
[2026-06-08T08:51:29] Searching for fusions with >=4 spliced events (remaining=6081)
[2026-06-08T08:51:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2495)
[2026-06-08T08:51:44] Filtering fusions with anchors <=23nt (remaining=2021)
[2026-06-08T08:51:45] Filtering end-to-end fusions with low support (remaining=1958)
[2026-06-08T08:51:46] Filtering fusions with no coverage around the breakpoints (remaining=1913)
[2026-06-08T08:51:46] Indexing gene sequences 
[2026-06-08T08:51:53] Filtering genes with >=30% identity (remaining=651)
[2026-06-08T08:51:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=392)
[2026-06-08T08:52:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=287)
[2026-06-08T08:52:02] Searching for additional isoforms (remaining=430)
[2026-06-08T08:52:03] Assigning confidence scores to events 
[2026-06-08T08:52:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:07] Writing fusions to file 'FFPE_HD789_01_RNA_13_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:10] Writing discarded fusions to file 'FFPE_HD789_01_RNA_13_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:38] Freeing resources
[2026-06-08T08:52:54] Done (elapsed time=00:11:25, CPU time=00:11:24, peak memory=14.3gb)