[2026-05-28T22:22:51] Launching Arriba 2.4.0
[2026-05-28T22:22:51] Loading assembly from 'ref_genome.fa' 
[2026-05-28T22:23:09] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T22:23:14] Reading chimeric alignments from 'A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=11029800)
[2026-05-28T22:36:13] Marking multi-mapping alignments (marked=7247393)
[2026-05-28T22:36:19] Detecting strandedness (reverse)
[2026-05-28T22:36:19] Assigning strands to alignments 
[2026-05-28T22:36:22] Annotating alignments 
[2026-05-28T22:37:20] Filtering duplicates (remaining=8047201)
[2026-05-28T22:37:34] 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)
[2026-05-28T22:37:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7494503)
[2026-05-28T22:37:40] Filtering viral contigs with expression lower than the top 5 (remaining=7494503)
[2026-05-28T22:37:47] Filtering viral contigs with less than 5% coverage (remaining=7494503)
[2026-05-28T22:37:51] Estimating fragment length (mate gap mean=-85.2914, mate gap stddev=29.5598, read length mean=128.962)
[2026-05-28T22:37:51] Filtering read-through fragments with a distance <=10000bp (remaining=7102839)
[2026-05-28T22:37:54] Filtering inconsistently clipped mates (remaining=6976532)
[2026-05-28T22:37:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6673021)
[2026-05-28T22:38:03] Filtering fragments with small insert size (remaining=6671736)
[2026-05-28T22:38:06] Filtering alignments with long gaps (remaining=6671735)
[2026-05-28T22:38:09] Filtering fragments with both mates in the same gene (remaining=6670491)
[2026-05-28T22:38:12] Filtering fusions arising from hairpin structures (remaining=6247554)
[2026-05-28T22:38:17] Filtering reads with a mismatch p-value <=0.01 (remaining=3075841)
[2026-05-28T22:38:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=1319547)
[2026-05-28T22:38:59] Finding fusions and counting supporting reads (total=1045361)
[2026-05-28T22:39:31] Merging adjacent fusion breakpoints (remaining=1038814)
[2026-05-28T22:39:34] Filtering multi-mapping fusions by alignment score and read support (remaining=641402)
[2026-05-28T22:40:27] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T22:40:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=638704)
[2026-05-28T22:40:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=408049)
[2026-05-28T22:40:44] Filtering fusions with <2 supporting reads (remaining=35942)
[2026-05-28T22:40:45] Filtering fusions with an e-value >=0.3 (remaining=7499)
[2026-05-28T22:40:47] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7558)
[2026-05-28T22:40:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7436)
[2026-05-28T22:40:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7440)
[2026-05-28T22:40:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6964)
[2026-05-28T22:41:06] Searching for fusions with spliced split reads (remaining=6986)
[2026-05-28T22:41:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=4344)
[2026-05-28T22:41:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4297)
[2026-05-28T22:41:19] Searching for fusions with >=4 spliced events (remaining=5490)
[2026-05-28T22:41:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2544)
[2026-05-28T22:41:53] Filtering fusions with anchors <=23nt (remaining=2033)
[2026-05-28T22:41:54] Filtering end-to-end fusions with low support (remaining=1990)
[2026-05-28T22:41:55] Filtering fusions with no coverage around the breakpoints (remaining=1966)
[2026-05-28T22:41:56] Indexing gene sequences 
[2026-05-28T22:42:08] Filtering genes with >=30% identity (remaining=541)
[2026-05-28T22:42:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=235)
[2026-05-28T22:42:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=194)
[2026-05-28T22:42:28] Searching for additional isoforms (remaining=275)
[2026-05-28T22:42:30] Assigning confidence scores to events 
[2026-05-28T22:42:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T22:42:37] Writing fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T22:42:41] Writing discarded fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T22:43:47] Freeing resources
[2026-05-28T22:44:21] Done (elapsed time=00:21:30, CPU time=00:21:29, peak memory=16gb)