[2026-06-08T08:28:59] Launching Arriba 2.4.0
[2026-06-08T08:28:59] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:12] Reading chimeric alignments from 'FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=11349652)
[2026-06-08T08:35:47] Marking multi-mapping alignments (marked=7459590)
[2026-06-08T08:35:52] Detecting strandedness (reverse)
[2026-06-08T08:35:52] Assigning strands to alignments 
[2026-06-08T08:35:54] Annotating alignments 
[2026-06-08T08:36:29] Filtering duplicates (remaining=7061589)
[2026-06-08T08:36:36] 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=6580239)
[2026-06-08T08:36:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6580239)
[2026-06-08T08:36:40] Filtering viral contigs with expression lower than the top 5 (remaining=6580239)
[2026-06-08T08:36:45] Filtering viral contigs with less than 5% coverage (remaining=6580239)
[2026-06-08T08:36:48] Estimating fragment length (mate gap mean=-87.4054, mate gap stddev=32.1739, read length mean=130.667)
[2026-06-08T08:36:48] Filtering read-through fragments with a distance <=10000bp (remaining=6317512)
[2026-06-08T08:36:50] Filtering inconsistently clipped mates (remaining=6210094)
[2026-06-08T08:36:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5920511)
[2026-06-08T08:36:59] Filtering fragments with small insert size (remaining=5919439)
[2026-06-08T08:37:04] Filtering alignments with long gaps (remaining=5919439)
[2026-06-08T08:37:07] Filtering fragments with both mates in the same gene (remaining=5918226)
[2026-06-08T08:37:10] Filtering fusions arising from hairpin structures (remaining=5543115)
[2026-06-08T08:37:13] Filtering reads with a mismatch p-value <=0.01 (remaining=2543781)
[2026-06-08T08:37:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=950851)
[2026-06-08T08:37:40] Finding fusions and counting supporting reads (total=741842)
[2026-06-08T08:37:56] Merging adjacent fusion breakpoints (remaining=734373)
[2026-06-08T08:37:58] Filtering multi-mapping fusions by alignment score and read support (remaining=454962)
[2026-06-08T08:38:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:38:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=452691)
[2026-06-08T08:38:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=264019)
[2026-06-08T08:38:43] Filtering fusions with <2 supporting reads (remaining=28927)
[2026-06-08T08:38:44] Filtering fusions with an e-value >=0.3 (remaining=8174)
[2026-06-08T08:38:45] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8220)
[2026-06-08T08:38:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8085)
[2026-06-08T08:38:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8120)
[2026-06-08T08:38:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6181)
[2026-06-08T08:38:57] Searching for fusions with spliced split reads (remaining=6300)
[2026-06-08T08:39:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=3832)
[2026-06-08T08:39:04] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3800)
[2026-06-08T08:39:05] Searching for fusions with >=4 spliced events (remaining=4471)
[2026-06-08T08:39:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1854)
[2026-06-08T08:39:24] Filtering fusions with anchors <=23nt (remaining=1137)
[2026-06-08T08:39:25] Filtering end-to-end fusions with low support (remaining=1115)
[2026-06-08T08:39:25] Filtering fusions with no coverage around the breakpoints (remaining=1095)
[2026-06-08T08:39:26] Indexing gene sequences 
[2026-06-08T08:39:31] Filtering genes with >=30% identity (remaining=278)
[2026-06-08T08:39:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=96)
[2026-06-08T08:39:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=94)
[2026-06-08T08:39:38] Searching for additional isoforms (remaining=125)
[2026-06-08T08:39:39] Assigning confidence scores to events 
[2026-06-08T08:39:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:39:43] Writing fusions to file 'FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:39:44] Writing discarded fusions to file 'FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:15] Freeing resources
[2026-06-08T08:40:35] Done (elapsed time=00:11:36, CPU time=00:11:34, peak memory=16gb)