[2026-06-08T08:33:25] Launching Arriba 2.4.0
[2026-06-08T08:33:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:33:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:33:43] Reading chimeric alignments from 'FFPE_V4_0002_RNA_0002_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11523070)
[2026-06-08T08:41:51] Marking multi-mapping alignments (marked=8014712)
[2026-06-08T08:41:55] Detecting strandedness (reverse)
[2026-06-08T08:41:55] Assigning strands to alignments 
[2026-06-08T08:41:58] Annotating alignments 
[2026-06-08T08:42:34] Filtering duplicates (remaining=6282069)
[2026-06-08T08:42:41] 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=5652109)
[2026-06-08T08:42:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5652109)
[2026-06-08T08:42:46] Filtering viral contigs with expression lower than the top 5 (remaining=5652109)
[2026-06-08T08:42:51] Filtering viral contigs with less than 5% coverage (remaining=5652109)
[2026-06-08T08:42:53] Estimating fragment length (mate gap mean=-85.0715, mate gap stddev=32.0524, read length mean=129.433)
[2026-06-08T08:42:54] Filtering read-through fragments with a distance <=10000bp (remaining=5429803)
[2026-06-08T08:42:56] Filtering inconsistently clipped mates (remaining=5324970)
[2026-06-08T08:42:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5124366)
[2026-06-08T08:43:03] Filtering fragments with small insert size (remaining=5123405)
[2026-06-08T08:43:05] Filtering alignments with long gaps (remaining=5123405)
[2026-06-08T08:43:07] Filtering fragments with both mates in the same gene (remaining=5122365)
[2026-06-08T08:43:10] Filtering fusions arising from hairpin structures (remaining=4786365)
[2026-06-08T08:43:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2070847)
[2026-06-08T08:43:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=824406)
[2026-06-08T08:43:39] Finding fusions and counting supporting reads (total=617894)
[2026-06-08T08:43:57] Merging adjacent fusion breakpoints (remaining=612352)
[2026-06-08T08:43:59] Filtering multi-mapping fusions by alignment score and read support (remaining=371977)
[2026-06-08T08:44:33] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=369514)
[2026-06-08T08:44:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=221359)
[2026-06-08T08:44:40] Filtering fusions with <2 supporting reads (remaining=28844)
[2026-06-08T08:44:41] Filtering fusions with an e-value >=0.3 (remaining=9566)
[2026-06-08T08:44:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9609)
[2026-06-08T08:44:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9525)
[2026-06-08T08:44:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9530)
[2026-06-08T08:44:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6996)
[2026-06-08T08:44:52] Searching for fusions with spliced split reads (remaining=7101)
[2026-06-08T08:44:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=4030)
[2026-06-08T08:44:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3988)
[2026-06-08T08:44:59] Searching for fusions with >=4 spliced events (remaining=4751)
[2026-06-08T08:45:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1817)
[2026-06-08T08:45:21] Filtering fusions with anchors <=23nt (remaining=1306)
[2026-06-08T08:45:21] Filtering end-to-end fusions with low support (remaining=1240)
[2026-06-08T08:45:22] Filtering fusions with no coverage around the breakpoints (remaining=1207)
[2026-06-08T08:45:23] Indexing gene sequences 
[2026-06-08T08:45:28] Filtering genes with >=30% identity (remaining=352)
[2026-06-08T08:45:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=124)
[2026-06-08T08:45:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-08T08:45:35] Searching for additional isoforms (remaining=151)
[2026-06-08T08:45:36] Assigning confidence scores to events 
[2026-06-08T08:45:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:40] Writing fusions to file 'FFPE_V4_0002_RNA_0002_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:41] Writing discarded fusions to file 'FFPE_V4_0002_RNA_0002_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:08] Freeing resources
[2026-06-08T08:46:26] Done (elapsed time=00:13:01, CPU time=00:13:00, peak memory=16.3gb)