[2026-06-08T08:32:08] Launching Arriba 2.4.0
[2026-06-08T08:32:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:21] Reading chimeric alignments from 'A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=11029800)
[2026-06-08T08:39:55] Marking multi-mapping alignments (marked=7247393)
[2026-06-08T08:40:01] Detecting strandedness (reverse)
[2026-06-08T08:40:01] Assigning strands to alignments 
[2026-06-08T08:40:04] Annotating alignments 
[2026-06-08T08:41:01] Filtering duplicates (remaining=8047201)
[2026-06-08T08:41:13] 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=7494503)
[2026-06-08T08:41:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7494503)
[2026-06-08T08:41:20] Filtering viral contigs with expression lower than the top 5 (remaining=7494503)
[2026-06-08T08:41:28] Filtering viral contigs with less than 5% coverage (remaining=7494503)
[2026-06-08T08:41:31] Estimating fragment length (mate gap mean=-85.2914, mate gap stddev=29.5598, read length mean=128.962)
[2026-06-08T08:41:31] Filtering read-through fragments with a distance <=10000bp (remaining=7102839)
[2026-06-08T08:41:35] Filtering inconsistently clipped mates (remaining=6976532)
[2026-06-08T08:41:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6673021)
[2026-06-08T08:41:46] Filtering fragments with small insert size (remaining=6671736)
[2026-06-08T08:41:49] Filtering alignments with long gaps (remaining=6671735)
[2026-06-08T08:41:53] Filtering fragments with both mates in the same gene (remaining=6670491)
[2026-06-08T08:41:56] Filtering fusions arising from hairpin structures (remaining=6247554)
[2026-06-08T08:42:00] Filtering reads with a mismatch p-value <=0.01 (remaining=3075841)
[2026-06-08T08:42:19] Filtering reads with low entropy (k-mer content >=60%) (remaining=1319547)
[2026-06-08T08:42:34] Finding fusions and counting supporting reads (total=1045361)
[2026-06-08T08:43:07] Merging adjacent fusion breakpoints (remaining=1038814)
[2026-06-08T08:43:10] Filtering multi-mapping fusions by alignment score and read support (remaining=641402)
[2026-06-08T08:44:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=638704)
[2026-06-08T08:44:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=408049)
[2026-06-08T08:44:21] Filtering fusions with <2 supporting reads (remaining=35942)
[2026-06-08T08:44:23] Filtering fusions with an e-value >=0.3 (remaining=7499)
[2026-06-08T08:44:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7558)
[2026-06-08T08:44:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7436)
[2026-06-08T08:44:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7440)
[2026-06-08T08:44:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6964)
[2026-06-08T08:44:46] Searching for fusions with spliced split reads (remaining=6986)
[2026-06-08T08:44:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=4344)
[2026-06-08T08:45:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4297)
[2026-06-08T08:45:01] Searching for fusions with >=4 spliced events (remaining=5490)
[2026-06-08T08:45:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2544)
[2026-06-08T08:45:25] Filtering fusions with anchors <=23nt (remaining=2033)
[2026-06-08T08:45:27] Filtering end-to-end fusions with low support (remaining=1990)
[2026-06-08T08:45:28] Filtering fusions with no coverage around the breakpoints (remaining=1966)
[2026-06-08T08:45:30] Indexing gene sequences 
[2026-06-08T08:45:40] Filtering genes with >=30% identity (remaining=541)
[2026-06-08T08:45:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=235)
[2026-06-08T08:45:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=194)
[2026-06-08T08:45:57] Searching for additional isoforms (remaining=275)
[2026-06-08T08:46:00] Assigning confidence scores to events 
[2026-06-08T08:46:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:08] Writing fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:46:11] Writing discarded fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:15] Freeing resources
[2026-06-08T08:47:45] Done (elapsed time=00:15:37, CPU time=00:15:35, peak memory=15.9gb)