[2026-05-28T21:20:50] Launching Arriba 2.4.0
[2026-05-28T21:20:50] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:21:04] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:21:09] Reading chimeric alignments from '786-O_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=11778278)
[2026-05-28T21:29:30] Marking multi-mapping alignments (marked=7763656)
[2026-05-28T21:29:35] Detecting strandedness (reverse)
[2026-05-28T21:29:35] Assigning strands to alignments 
[2026-05-28T21:29:38] Annotating alignments 
[2026-05-28T21:30:15] Filtering duplicates (remaining=8617202)
[2026-05-28T21:30:24] 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=8056035)
[2026-05-28T21:30:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8056035)
[2026-05-28T21:30:28] Filtering viral contigs with expression lower than the top 5 (remaining=8056035)
[2026-05-28T21:30:33] Filtering viral contigs with less than 5% coverage (remaining=8056035)
[2026-05-28T21:30:36] Estimating fragment length (mate gap mean=-85.7933, mate gap stddev=30.4182, read length mean=130.498)
[2026-05-28T21:30:36] Filtering read-through fragments with a distance <=10000bp (remaining=7649034)
[2026-05-28T21:30:38] Filtering inconsistently clipped mates (remaining=7517165)
[2026-05-28T21:30:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7244597)
[2026-05-28T21:30:46] Filtering fragments with small insert size (remaining=7243326)
[2026-05-28T21:30:48] Filtering alignments with long gaps (remaining=7243326)
[2026-05-28T21:30:50] Filtering fragments with both mates in the same gene (remaining=7241911)
[2026-05-28T21:30:53] Filtering fusions arising from hairpin structures (remaining=6747494)
[2026-05-28T21:30:56] Filtering reads with a mismatch p-value <=0.01 (remaining=3141770)
[2026-05-28T21:31:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=1304292)
[2026-05-28T21:31:30] Finding fusions and counting supporting reads (total=1055690)
[2026-05-28T21:31:51] Merging adjacent fusion breakpoints (remaining=1047488)
[2026-05-28T21:31:53] Filtering multi-mapping fusions by alignment score and read support (remaining=658601)
[2026-05-28T21:32:31] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:32:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=655870)
[2026-05-28T21:32:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=394140)
[2026-05-28T21:32:43] Filtering fusions with <2 supporting reads (remaining=35954)
[2026-05-28T21:32:44] Filtering fusions with an e-value >=0.3 (remaining=7892)
[2026-05-28T21:32:45] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7927)
[2026-05-28T21:32:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7804)
[2026-05-28T21:32:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7804)
[2026-05-28T21:32:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7073)
[2026-05-28T21:32:59] Searching for fusions with spliced split reads (remaining=7099)
[2026-05-28T21:33:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=4334)
[2026-05-28T21:33:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4301)
[2026-05-28T21:33:08] Searching for fusions with >=4 spliced events (remaining=5401)
[2026-05-28T21:33:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2396)
[2026-05-28T21:33:27] Filtering fusions with anchors <=23nt (remaining=1921)
[2026-05-28T21:33:28] Filtering end-to-end fusions with low support (remaining=1868)
[2026-05-28T21:33:29] Filtering fusions with no coverage around the breakpoints (remaining=1850)
[2026-05-28T21:33:30] Indexing gene sequences 
[2026-05-28T21:33:38] Filtering genes with >=30% identity (remaining=557)
[2026-05-28T21:33:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=257)
[2026-05-28T21:33:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=215)
[2026-05-28T21:33:59] Searching for additional isoforms (remaining=298)
[2026-05-28T21:34:01] Assigning confidence scores to events 
[2026-05-28T21:34:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:34:06] Writing fusions to file '786-O_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:34:09] Writing discarded fusions to file '786-O_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:34:51] Freeing resources
[2026-05-28T21:35:11] Done (elapsed time=00:14:21, CPU time=00:14:20, peak memory=16.8gb)