[2026-05-28T20:38:04] Launching Arriba 2.4.0
[2026-05-28T20:38:04] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:38:20] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:38:27] Reading chimeric alignments from 'SkinN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=8376778)
[2026-05-28T20:41:48] Marking multi-mapping alignments (marked=6997713)
[2026-05-28T20:41:52] Detecting strandedness (no)
[2026-05-28T20:41:52] Annotating alignments 
[2026-05-28T20:42:31] Filtering duplicates (remaining=1670231)
[2026-05-28T20:42:35] 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=1249233)
[2026-05-28T20:42:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1249233)
[2026-05-28T20:42:39] Filtering viral contigs with expression lower than the top 5 (remaining=1249233)
[2026-05-28T20:42:42] Filtering viral contigs with less than 5% coverage (remaining=1249233)
[2026-05-28T20:42:44] Estimating fragment length (mate gap mean=-61.0177, mate gap stddev=29.2256, read length mean=95.991)
[2026-05-28T20:42:45] Filtering read-through fragments with a distance <=10000bp (remaining=1226736)
[2026-05-28T20:42:46] Filtering inconsistently clipped mates (remaining=1179181)
[2026-05-28T20:42:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1052312)
[2026-05-28T20:42:50] Filtering fragments with small insert size (remaining=1050438)
[2026-05-28T20:42:52] Filtering alignments with long gaps (remaining=1050438)
[2026-05-28T20:42:54] Filtering fragments with both mates in the same gene (remaining=1049448)
[2026-05-28T20:42:56] Filtering fusions arising from hairpin structures (remaining=976474)
[2026-05-28T20:42:57] Filtering reads with a mismatch p-value <=0.01 (remaining=239960)
[2026-05-28T20:43:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=97380)
[2026-05-28T20:43:05] Finding fusions and counting supporting reads (total=89984)
[2026-05-28T20:43:16] Merging adjacent fusion breakpoints (remaining=89258)
[2026-05-28T20:43:16] Filtering multi-mapping fusions by alignment score and read support (remaining=31918)
[2026-05-28T20:43:46] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:43:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=31214)
[2026-05-28T20:43:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=26248)
[2026-05-28T20:43:49] Filtering fusions with <2 supporting reads (remaining=930)
[2026-05-28T20:43:50] Filtering fusions with an e-value >=0.3 (remaining=255)
[2026-05-28T20:43:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=257)
[2026-05-28T20:43:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=176)
[2026-05-28T20:43:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=176)
[2026-05-28T20:43:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=171)
[2026-05-28T20:43:56] Searching for fusions with spliced split reads (remaining=179)
[2026-05-28T20:44:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=149)
[2026-05-28T20:44:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=147)
[2026-05-28T20:44:00] Searching for fusions with >=4 spliced events (remaining=149)
[2026-05-28T20:44:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=46)
[2026-05-28T20:44:22] Filtering fusions with anchors <=23nt (remaining=34)
[2026-05-28T20:44:22] Filtering end-to-end fusions with low support (remaining=33)
[2026-05-28T20:44:22] Filtering fusions with no coverage around the breakpoints (remaining=33)
[2026-05-28T20:44:23] Indexing gene sequences 
[2026-05-28T20:44:24] Filtering genes with >=30% identity (remaining=13)
[2026-05-28T20:44:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=2)
[2026-05-28T20:44:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=2)
[2026-05-28T20:44:25] Searching for additional isoforms (remaining=2)
[2026-05-28T20:44:25] Assigning confidence scores to events 
[2026-05-28T20:44:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:44:27] Writing fusions to file 'SkinN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:44:27] Writing discarded fusions to file 'SkinN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:44:40] Freeing resources
[2026-05-28T20:44:58] Done (elapsed time=00:06:54, CPU time=00:06:52, peak memory=12.5gb)