[2026-06-03T20:18:50] Launching Arriba 2.4.0
[2026-06-03T20:18:50] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:18:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:19:02] Reading chimeric alignments from 'FFPE_V4_0002_RNA_0002_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11523070)
[2026-06-03T20:25:52] Marking multi-mapping alignments (marked=8014712)
[2026-06-03T20:25:56] Detecting strandedness (reverse)
[2026-06-03T20:25:56] Assigning strands to alignments 
[2026-06-03T20:25:58] Annotating alignments 
[2026-06-03T20:26:35] Filtering duplicates (remaining=6282069)
[2026-06-03T20:26:42] 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)
[2026-06-03T20:26:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5652109)
[2026-06-03T20:26:46] Filtering viral contigs with expression lower than the top 5 (remaining=5652109)
[2026-06-03T20:26:51] Filtering viral contigs with less than 5% coverage (remaining=5652109)
[2026-06-03T20:26:54] Estimating fragment length (mate gap mean=-85.0715, mate gap stddev=32.0524, read length mean=129.433)
[2026-06-03T20:26:54] Filtering read-through fragments with a distance <=10000bp (remaining=5429803)
[2026-06-03T20:26:56] Filtering inconsistently clipped mates (remaining=5324970)
[2026-06-03T20:26:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5124366)
[2026-06-03T20:27:03] Filtering fragments with small insert size (remaining=5123405)
[2026-06-03T20:27:05] Filtering alignments with long gaps (remaining=5123405)
[2026-06-03T20:27:07] Filtering fragments with both mates in the same gene (remaining=5122365)
[2026-06-03T20:27:09] Filtering fusions arising from hairpin structures (remaining=4786365)
[2026-06-03T20:27:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2070847)
[2026-06-03T20:27:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=824406)
[2026-06-03T20:27:35] Finding fusions and counting supporting reads (total=617894)
[2026-06-03T20:27:51] Merging adjacent fusion breakpoints (remaining=612352)
[2026-06-03T20:27:53] Filtering multi-mapping fusions by alignment score and read support (remaining=371977)
[2026-06-03T20:28:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:28:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=369514)
[2026-06-03T20:28:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=221359)
[2026-06-03T20:28:35] Filtering fusions with <2 supporting reads (remaining=28844)
[2026-06-03T20:28:36] Filtering fusions with an e-value >=0.3 (remaining=9566)
[2026-06-03T20:28:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9609)
[2026-06-03T20:28:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9525)
[2026-06-03T20:28:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9530)
[2026-06-03T20:28:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6996)
[2026-06-03T20:28:47] Searching for fusions with spliced split reads (remaining=7101)
[2026-06-03T20:28:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=4030)
[2026-06-03T20:28:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3988)
[2026-06-03T20:28:54] Searching for fusions with >=4 spliced events (remaining=4751)
[2026-06-03T20:28:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1817)
[2026-06-03T20:29:11] Filtering fusions with anchors <=23nt (remaining=1306)
[2026-06-03T20:29:12] Filtering end-to-end fusions with low support (remaining=1240)
[2026-06-03T20:29:13] Filtering fusions with no coverage around the breakpoints (remaining=1207)
[2026-06-03T20:29:13] Indexing gene sequences 
[2026-06-03T20:29:18] Filtering genes with >=30% identity (remaining=352)
[2026-06-03T20:29:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=124)
[2026-06-03T20:29:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-03T20:29:25] Searching for additional isoforms (remaining=151)
[2026-06-03T20:29:26] Assigning confidence scores to events 
[2026-06-03T20:29:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:29:29] Writing fusions to file 'FFPE_V4_0002_RNA_0002_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:29:30] Writing discarded fusions to file 'FFPE_V4_0002_RNA_0002_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:29:53] Freeing resources
[2026-06-03T20:30:11] Done (elapsed time=00:11:21, CPU time=00:11:19, peak memory=16.3gb)