[2026-06-08T08:26:42] Launching Arriba 2.4.0
[2026-06-08T08:26:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:55] Reading chimeric alignments from 'SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=13148700)
[2026-06-08T08:32:03] Marking multi-mapping alignments (marked=10066288)
[2026-06-08T08:32:07] Detecting strandedness (reverse)
[2026-06-08T08:32:07] Assigning strands to alignments 
[2026-06-08T08:32:09] Annotating alignments 
[2026-06-08T08:32:45] Filtering duplicates (remaining=2695132)
[2026-06-08T08:32:50] 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=2321688)
[2026-06-08T08:32:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2321688)
[2026-06-08T08:32:55] Filtering viral contigs with expression lower than the top 5 (remaining=2321688)
[2026-06-08T08:32:59] Filtering viral contigs with less than 5% coverage (remaining=2321688)
[2026-06-08T08:33:01] Estimating fragment length (mate gap mean=-73.72, mate gap stddev=28.5823, read length mean=110.192)
[2026-06-08T08:33:02] Filtering read-through fragments with a distance <=10000bp (remaining=2259554)
[2026-06-08T08:33:04] Filtering inconsistently clipped mates (remaining=2195345)
[2026-06-08T08:33:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1912447)
[2026-06-08T08:33:09] Filtering fragments with small insert size (remaining=1911199)
[2026-06-08T08:33:11] Filtering alignments with long gaps (remaining=1911199)
[2026-06-08T08:33:14] Filtering fragments with both mates in the same gene (remaining=1910154)
[2026-06-08T08:33:16] Filtering fusions arising from hairpin structures (remaining=1817623)
[2026-06-08T08:33:18] Filtering reads with a mismatch p-value <=0.01 (remaining=579842)
[2026-06-08T08:33:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=200496)
[2026-06-08T08:33:29] Finding fusions and counting supporting reads (total=197225)
[2026-06-08T08:33:42] Merging adjacent fusion breakpoints (remaining=195892)
[2026-06-08T08:33:43] Filtering multi-mapping fusions by alignment score and read support (remaining=76362)
[2026-06-08T08:34:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=75168)
[2026-06-08T08:34:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=58930)
[2026-06-08T08:34:19] Filtering fusions with <2 supporting reads (remaining=2348)
[2026-06-08T08:34:20] Filtering fusions with an e-value >=0.3 (remaining=553)
[2026-06-08T08:34:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=558)
[2026-06-08T08:34:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=452)
[2026-06-08T08:34:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=452)
[2026-06-08T08:34:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=452)
[2026-06-08T08:34:28] Searching for fusions with spliced split reads (remaining=484)
[2026-06-08T08:34:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=381)
[2026-06-08T08:34:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=374)
[2026-06-08T08:34:33] Searching for fusions with >=4 spliced events (remaining=385)
[2026-06-08T08:34:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=96)
[2026-06-08T08:34:45] Filtering fusions with anchors <=23nt (remaining=67)
[2026-06-08T08:34:46] Filtering end-to-end fusions with low support (remaining=65)
[2026-06-08T08:34:46] Filtering fusions with no coverage around the breakpoints (remaining=64)
[2026-06-08T08:34:46] Indexing gene sequences 
[2026-06-08T08:34:47] Filtering genes with >=30% identity (remaining=27)
[2026-06-08T08:34:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=5)
[2026-06-08T08:34:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=5)
[2026-06-08T08:34:49] Searching for additional isoforms (remaining=5)
[2026-06-08T08:34:49] Assigning confidence scores to events 
[2026-06-08T08:34:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:51] Writing fusions to file 'SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:51] Writing discarded fusions to file 'SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:03] Freeing resources
[2026-06-08T08:35:18] Done (elapsed time=00:08:36, CPU time=00:08:35, peak memory=17.3gb)