[2026-06-08T08:55:04] Launching Arriba 2.4.0
[2026-06-08T08:55:04] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:55:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:55:17] Reading chimeric alignments from 'U118MG_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=11485957)
[2026-06-08T09:02:21] Marking multi-mapping alignments (marked=7494971)
[2026-06-08T09:02:26] Detecting strandedness (reverse)
[2026-06-08T09:02:26] Assigning strands to alignments 
[2026-06-08T09:02:28] Annotating alignments 
[2026-06-08T09:03:07] Filtering duplicates (remaining=8364107)
[2026-06-08T09:03:15] 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=7711877)
[2026-06-08T09:03:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7711877)
[2026-06-08T09:03:20] Filtering viral contigs with expression lower than the top 5 (remaining=7711877)
[2026-06-08T09:03:25] Filtering viral contigs with less than 5% coverage (remaining=7711877)
[2026-06-08T09:03:28] Estimating fragment length (mate gap mean=-85.7797, mate gap stddev=30.8408, read length mean=130.12)
[2026-06-08T09:03:28] Filtering read-through fragments with a distance <=10000bp (remaining=7300862)
[2026-06-08T09:03:30] Filtering inconsistently clipped mates (remaining=7183043)
[2026-06-08T09:03:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6937589)
[2026-06-08T09:03:37] Filtering fragments with small insert size (remaining=6936280)
[2026-06-08T09:03:40] Filtering alignments with long gaps (remaining=6936280)
[2026-06-08T09:03:42] Filtering fragments with both mates in the same gene (remaining=6934700)
[2026-06-08T09:03:44] Filtering fusions arising from hairpin structures (remaining=6516839)
[2026-06-08T09:03:47] Filtering reads with a mismatch p-value <=0.01 (remaining=3028939)
[2026-06-08T09:04:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=1294027)
[2026-06-08T09:04:18] Finding fusions and counting supporting reads (total=1008540)
[2026-06-08T09:04:38] Merging adjacent fusion breakpoints (remaining=1001232)
[2026-06-08T09:04:41] Filtering multi-mapping fusions by alignment score and read support (remaining=650870)
[2026-06-08T09:05:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:05:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=647831)
[2026-06-08T09:05:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=379329)
[2026-06-08T09:05:31] Filtering fusions with <2 supporting reads (remaining=37614)
[2026-06-08T09:05:32] Filtering fusions with an e-value >=0.3 (remaining=8086)
[2026-06-08T09:05:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8142)
[2026-06-08T09:05:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8018)
[2026-06-08T09:05:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8023)
[2026-06-08T09:05:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7141)
[2026-06-08T09:05:47] Searching for fusions with spliced split reads (remaining=7165)
[2026-06-08T09:05:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=4333)
[2026-06-08T09:05:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4297)
[2026-06-08T09:05:56] Searching for fusions with >=4 spliced events (remaining=5356)
[2026-06-08T09:05:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2222)
[2026-06-08T09:06:12] Filtering fusions with anchors <=23nt (remaining=1796)
[2026-06-08T09:06:13] Filtering end-to-end fusions with low support (remaining=1765)
[2026-06-08T09:06:14] Filtering fusions with no coverage around the breakpoints (remaining=1743)
[2026-06-08T09:06:16] Indexing gene sequences 
[2026-06-08T09:06:23] Filtering genes with >=30% identity (remaining=609)
[2026-06-08T09:06:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=364)
[2026-06-08T09:06:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=281)
[2026-06-08T09:06:44] Searching for additional isoforms (remaining=400)
[2026-06-08T09:06:46] Assigning confidence scores to events 
[2026-06-08T09:06:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:06:51] Writing fusions to file 'U118MG_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-06-08T09:06:55] Writing discarded fusions to file 'U118MG_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T09:07:33] Freeing resources
[2026-06-08T09:07:53] Done (elapsed time=00:12:49, CPU time=00:12:48, peak memory=16.4gb)