[2026-05-28T21:19:17] Launching Arriba 2.4.0
[2026-05-28T21:19:17] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:19:25] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:19:29] Reading chimeric alignments from 'A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=11025666)
[2026-05-28T21:26:28] Marking multi-mapping alignments (marked=7327549)
[2026-05-28T21:26:33] Detecting strandedness (reverse)
[2026-05-28T21:26:33] Assigning strands to alignments 
[2026-05-28T21:26:35] Annotating alignments 
[2026-05-28T21:27:18] Filtering duplicates (remaining=7760595)
[2026-05-28T21:27:27] 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)
[2026-05-28T21:27:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7220640)
[2026-05-28T21:27:32] Filtering viral contigs with expression lower than the top 5 (remaining=7220640)
[2026-05-28T21:27:38] Filtering viral contigs with less than 5% coverage (remaining=7220640)
[2026-05-28T21:27:41] Estimating fragment length (mate gap mean=-83.6211, mate gap stddev=29.2578, read length mean=126.931)
[2026-05-28T21:27:41] Filtering read-through fragments with a distance <=10000bp (remaining=6880858)
[2026-05-28T21:27:43] Filtering inconsistently clipped mates (remaining=6765400)
[2026-05-28T21:27:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6481463)
[2026-05-28T21:27:51] Filtering fragments with small insert size (remaining=6480190)
[2026-05-28T21:27:54] Filtering alignments with long gaps (remaining=6480189)
[2026-05-28T21:27:56] Filtering fragments with both mates in the same gene (remaining=6478935)
[2026-05-28T21:27:59] Filtering fusions arising from hairpin structures (remaining=6129180)
[2026-05-28T21:28:02] Filtering reads with a mismatch p-value <=0.01 (remaining=2967007)
[2026-05-28T21:28:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=1181205)
[2026-05-28T21:28:30] Finding fusions and counting supporting reads (total=934189)
[2026-05-28T21:28:52] Merging adjacent fusion breakpoints (remaining=928444)
[2026-05-28T21:28:55] Filtering multi-mapping fusions by alignment score and read support (remaining=575535)
[2026-05-28T21:29:35] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:29:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=573116)
[2026-05-28T21:29:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=361039)
[2026-05-28T21:29:50] Filtering fusions with <2 supporting reads (remaining=31865)
[2026-05-28T21:29:51] Filtering fusions with an e-value >=0.3 (remaining=6581)
[2026-05-28T21:29:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6646)
[2026-05-28T21:29:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6522)
[2026-05-28T21:29:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6526)
[2026-05-28T21:30:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6223)
[2026-05-28T21:30:07] Searching for fusions with spliced split reads (remaining=6346)
[2026-05-28T21:30:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=4093)
[2026-05-28T21:30:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4049)
[2026-05-28T21:30:18] Searching for fusions with >=4 spliced events (remaining=5125)
[2026-05-28T21:30:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2353)
[2026-05-28T21:30:38] Filtering fusions with anchors <=23nt (remaining=1914)
[2026-05-28T21:30:39] Filtering end-to-end fusions with low support (remaining=1866)
[2026-05-28T21:30:40] Filtering fusions with no coverage around the breakpoints (remaining=1844)
[2026-05-28T21:30:41] Indexing gene sequences 
[2026-05-28T21:30:50] Filtering genes with >=30% identity (remaining=539)
[2026-05-28T21:30:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=244)
[2026-05-28T21:31:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=203)
[2026-05-28T21:31:02] Searching for additional isoforms (remaining=261)
[2026-05-28T21:31:05] Assigning confidence scores to events 
[2026-05-28T21:31:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:31:11] Writing fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-05-28T21:31:15] Writing discarded fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-05-28T21:32:05] Freeing resources
[2026-05-28T21:32:28] Done (elapsed time=00:13:11, CPU time=00:13:09, peak memory=15.7gb)