[2026-06-08T08:46:05] Launching Arriba 2.4.0
[2026-06-08T08:46:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:24] Reading chimeric alignments from 'A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=11025666)
[2026-06-08T08:54:28] Marking multi-mapping alignments (marked=7327549)
[2026-06-08T08:54:33] Detecting strandedness (reverse)
[2026-06-08T08:54:33] Assigning strands to alignments 
[2026-06-08T08:54:35] Annotating alignments 
[2026-06-08T08:55:10] Filtering duplicates (remaining=7760595)
[2026-06-08T08:55:18] 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=7220640)
[2026-06-08T08:55:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7220640)
[2026-06-08T08:55:23] Filtering viral contigs with expression lower than the top 5 (remaining=7220640)
[2026-06-08T08:55:27] Filtering viral contigs with less than 5% coverage (remaining=7220640)
[2026-06-08T08:55:30] Estimating fragment length (mate gap mean=-83.6211, mate gap stddev=29.2578, read length mean=126.931)
[2026-06-08T08:55:30] Filtering read-through fragments with a distance <=10000bp (remaining=6880858)
[2026-06-08T08:55:32] Filtering inconsistently clipped mates (remaining=6765400)
[2026-06-08T08:55:34] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6481463)
[2026-06-08T08:55:39] Filtering fragments with small insert size (remaining=6480190)
[2026-06-08T08:55:41] Filtering alignments with long gaps (remaining=6480189)
[2026-06-08T08:55:43] Filtering fragments with both mates in the same gene (remaining=6478935)
[2026-06-08T08:55:46] Filtering fusions arising from hairpin structures (remaining=6129180)
[2026-06-08T08:55:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2967007)
[2026-06-08T08:56:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1181205)
[2026-06-08T08:56:17] Finding fusions and counting supporting reads (total=934189)
[2026-06-08T08:56:36] Merging adjacent fusion breakpoints (remaining=928444)
[2026-06-08T08:56:38] Filtering multi-mapping fusions by alignment score and read support (remaining=575535)
[2026-06-08T08:57:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=573116)
[2026-06-08T08:57:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=361039)
[2026-06-08T08:57:23] Filtering fusions with <2 supporting reads (remaining=31865)
[2026-06-08T08:57:24] Filtering fusions with an e-value >=0.3 (remaining=6581)
[2026-06-08T08:57:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6646)
[2026-06-08T08:57:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6522)
[2026-06-08T08:57:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6526)
[2026-06-08T08:57:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6223)
[2026-06-08T08:57:37] Searching for fusions with spliced split reads (remaining=6346)
[2026-06-08T08:57:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=4093)
[2026-06-08T08:57:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4049)
[2026-06-08T08:57:46] Searching for fusions with >=4 spliced events (remaining=5125)
[2026-06-08T08:57:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2353)
[2026-06-08T08:58:05] Filtering fusions with anchors <=23nt (remaining=1914)
[2026-06-08T08:58:05] Filtering end-to-end fusions with low support (remaining=1866)
[2026-06-08T08:58:06] Filtering fusions with no coverage around the breakpoints (remaining=1844)
[2026-06-08T08:58:07] Indexing gene sequences 
[2026-06-08T08:58:15] Filtering genes with >=30% identity (remaining=539)
[2026-06-08T08:58:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=244)
[2026-06-08T08:58:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=203)
[2026-06-08T08:58:27] Searching for additional isoforms (remaining=261)
[2026-06-08T08:58:28] Assigning confidence scores to events 
[2026-06-08T08:58:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:33] Writing fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:58:36] Writing discarded fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:14] Freeing resources
[2026-06-08T08:59:33] Done (elapsed time=00:13:28, CPU time=00:13:27, peak memory=15.8gb)