[2026-06-08T08:36:35] Launching Arriba 2.4.0
[2026-06-08T08:36:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:54] Reading chimeric alignments from 'FFPE_HD789_01_RNA_13_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10464539)
[2026-06-08T08:46:03] Marking multi-mapping alignments (marked=6473785)
[2026-06-08T08:46:07] Detecting strandedness (reverse)
[2026-06-08T08:46:07] Assigning strands to alignments 
[2026-06-08T08:46:09] Annotating alignments 
[2026-06-08T08:46:42] Filtering duplicates (remaining=7192329)
[2026-06-08T08:46:50] 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=6887316)
[2026-06-08T08:46:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6887316)
[2026-06-08T08:46:54] Filtering viral contigs with expression lower than the top 5 (remaining=6887316)
[2026-06-08T08:46:59] Filtering viral contigs with less than 5% coverage (remaining=6887316)
[2026-06-08T08:47:01] Estimating fragment length (mate gap mean=-83.1817, mate gap stddev=34.5064, read length mean=140.478)
[2026-06-08T08:47:01] Filtering read-through fragments with a distance <=10000bp (remaining=6600212)
[2026-06-08T08:47:03] Filtering inconsistently clipped mates (remaining=6522278)
[2026-06-08T08:47:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6327745)
[2026-06-08T08:47:10] Filtering fragments with small insert size (remaining=6327331)
[2026-06-08T08:47:12] Filtering alignments with long gaps (remaining=6327331)
[2026-06-08T08:47:14] Filtering fragments with both mates in the same gene (remaining=6326166)
[2026-06-08T08:47:16] Filtering fusions arising from hairpin structures (remaining=5948689)
[2026-06-08T08:47:18] Filtering reads with a mismatch p-value <=0.01 (remaining=3246156)
[2026-06-08T08:47:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=970272)
[2026-06-08T08:47:47] Finding fusions and counting supporting reads (total=697675)
[2026-06-08T08:48:04] Merging adjacent fusion breakpoints (remaining=689856)
[2026-06-08T08:48:06] Filtering multi-mapping fusions by alignment score and read support (remaining=465769)
[2026-06-08T08:48:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=460976)
[2026-06-08T08:48:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=260527)
[2026-06-08T08:48:51] Filtering fusions with <2 supporting reads (remaining=45097)
[2026-06-08T08:48:51] Filtering fusions with an e-value >=0.3 (remaining=18800)
[2026-06-08T08:48:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=18857)
[2026-06-08T08:48:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=18730)
[2026-06-08T08:48:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=18736)
[2026-06-08T08:48:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10681)
[2026-06-08T08:49:03] Searching for fusions with spliced split reads (remaining=10712)
[2026-06-08T08:49:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=5287)
[2026-06-08T08:49:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5243)
[2026-06-08T08:49:11] Searching for fusions with >=4 spliced events (remaining=6426)
[2026-06-08T08:49:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2620)
[2026-06-08T08:49:30] Filtering fusions with anchors <=23nt (remaining=2131)
[2026-06-08T08:49:31] Filtering end-to-end fusions with low support (remaining=2056)
[2026-06-08T08:49:32] Filtering fusions with no coverage around the breakpoints (remaining=2000)
[2026-06-08T08:49:32] Indexing gene sequences 
[2026-06-08T08:49:41] Filtering genes with >=30% identity (remaining=721)
[2026-06-08T08:49:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=438)
[2026-06-08T08:49:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=296)
[2026-06-08T08:49:51] Searching for additional isoforms (remaining=443)
[2026-06-08T08:49:53] Assigning confidence scores to events 
[2026-06-08T08:49:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:56] Writing fusions to file 'FFPE_HD789_01_RNA_13_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:01] Writing discarded fusions to file 'FFPE_HD789_01_RNA_13_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:46] Freeing resources
[2026-06-08T08:51:12] Done (elapsed time=00:14:37, CPU time=00:14:36, peak memory=15gb)