[2026-06-08T07:30:22] Launching Arriba 2.4.0
[2026-06-08T07:30:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:30:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:30:48] Reading chimeric alignments from 'EndoN_FFPE_L05_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=2618961)
[2026-06-08T07:32:06] Marking multi-mapping alignments (marked=2077802)
[2026-06-08T07:32:07] Detecting strandedness (reverse)
[2026-06-08T07:32:07] Assigning strands to alignments 
[2026-06-08T07:32:07] Annotating alignments 
[2026-06-08T07:32:18] Filtering duplicates (remaining=784015)
[2026-06-08T07:32:20] 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=685505)
[2026-06-08T07:32:21] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=685505)
[2026-06-08T07:32:21] Filtering viral contigs with expression lower than the top 5 (remaining=685505)
[2026-06-08T07:32:22] Filtering viral contigs with less than 5% coverage (remaining=685505)
[2026-06-08T07:32:23] Estimating fragment length (mate gap mean=-54.7048, mate gap stddev=27.4711, read length mean=91.0399)
[2026-06-08T07:32:24] Filtering read-through fragments with a distance <=10000bp (remaining=673854)
[2026-06-08T07:32:24] Filtering inconsistently clipped mates (remaining=641551)
[2026-06-08T07:32:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=570130)
[2026-06-08T07:32:25] Filtering fragments with small insert size (remaining=569021)
[2026-06-08T07:32:26] Filtering alignments with long gaps (remaining=569021)
[2026-06-08T07:32:26] Filtering fragments with both mates in the same gene (remaining=568396)
[2026-06-08T07:32:27] Filtering fusions arising from hairpin structures (remaining=529644)
[2026-06-08T07:32:28] Filtering reads with a mismatch p-value <=0.01 (remaining=105332)
[2026-06-08T07:32:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=44934)
[2026-06-08T07:32:31] Finding fusions and counting supporting reads (total=48665)
[2026-06-08T07:32:35] Merging adjacent fusion breakpoints (remaining=48504)
[2026-06-08T07:32:36] Filtering multi-mapping fusions by alignment score and read support (remaining=18664)
[2026-06-08T07:32:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:32:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=18335)
[2026-06-08T07:32:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=15480)
[2026-06-08T07:32:48] Filtering fusions with <2 supporting reads (remaining=232)
[2026-06-08T07:32:48] Filtering fusions with an e-value >=0.3 (remaining=87)
[2026-06-08T07:32:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=88)
[2026-06-08T07:32:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=62)
[2026-06-08T07:32:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=62)
[2026-06-08T07:32:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=61)
[2026-06-08T07:32:50] Searching for fusions with spliced split reads (remaining=62)
[2026-06-08T07:32:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=52)
[2026-06-08T07:32:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=51)
[2026-06-08T07:32:52] Searching for fusions with >=4 spliced events (remaining=51)
[2026-06-08T07:32:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15)
[2026-06-08T07:33:16] Filtering fusions with anchors <=23nt (remaining=13)
[2026-06-08T07:33:16] Filtering end-to-end fusions with low support (remaining=12)
[2026-06-08T07:33:16] Filtering fusions with no coverage around the breakpoints (remaining=11)
[2026-06-08T07:33:16] Indexing gene sequences 
[2026-06-08T07:33:16] Filtering genes with >=30% identity (remaining=7)
[2026-06-08T07:33:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=2)
[2026-06-08T07:33:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=2)
[2026-06-08T07:33:17] Searching for additional isoforms (remaining=2)
[2026-06-08T07:33:17] Assigning confidence scores to events 
[2026-06-08T07:33:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:33:18] Writing fusions to file 'EndoN_FFPE_L05_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:33:18] Writing discarded fusions to file 'EndoN_FFPE_L05_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:33:26] Freeing resources
[2026-06-08T07:33:30] Done (elapsed time=00:03:08, CPU time=00:03:06, peak memory=6.78gb)