[2026-06-08T09:06:59] Launching Arriba 2.4.0
[2026-06-08T09:06:59] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:07:14] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:07:19] Reading chimeric alignments from 'ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=29917134)
[2026-06-08T09:17:26] Marking multi-mapping alignments (marked=24164716)
[2026-06-08T09:17:37] Detecting strandedness (no)
[2026-06-08T09:17:37] Annotating alignments 
[2026-06-08T09:19:04] Filtering duplicates (remaining=4494343)
[2026-06-08T09:19:17] 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=3406653)
[2026-06-08T09:19:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3406653)
[2026-06-08T09:19:27] Filtering viral contigs with expression lower than the top 5 (remaining=3406653)
[2026-06-08T09:19:37] Filtering viral contigs with less than 5% coverage (remaining=3406653)
[2026-06-08T09:19:43] Estimating fragment length (mate gap mean=-74.5315, mate gap stddev=28.7702, read length mean=107.997)
[2026-06-08T09:19:43] Filtering read-through fragments with a distance <=10000bp (remaining=3266235)
[2026-06-08T09:19:48] Filtering inconsistently clipped mates (remaining=3156281)
[2026-06-08T09:19:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2912084)
[2026-06-08T09:19:59] Filtering fragments with small insert size (remaining=2909171)
[2026-06-08T09:20:04] Filtering alignments with long gaps (remaining=2909171)
[2026-06-08T09:20:09] Filtering fragments with both mates in the same gene (remaining=2908027)
[2026-06-08T09:20:14] Filtering fusions arising from hairpin structures (remaining=2746819)
[2026-06-08T09:20:19] Filtering reads with a mismatch p-value <=0.01 (remaining=736879)
[2026-06-08T09:20:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=326817)
[2026-06-08T09:20:41] Finding fusions and counting supporting reads (total=216117)
[2026-06-08T09:21:05] Merging adjacent fusion breakpoints (remaining=206071)
[2026-06-08T09:21:06] Filtering multi-mapping fusions by alignment score and read support (remaining=79690)
[2026-06-08T09:22:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:22:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=78125)
[2026-06-08T09:22:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=62506)
[2026-06-08T09:22:15] Filtering fusions with <2 supporting reads (remaining=8343)
[2026-06-08T09:22:16] Filtering fusions with an e-value >=0.3 (remaining=1383)
[2026-06-08T09:22:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1409)
[2026-06-08T09:22:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1199)
[2026-06-08T09:22:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1200)
[2026-06-08T09:22:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=815)
[2026-06-08T09:22:31] Searching for fusions with spliced split reads (remaining=839)
[2026-06-08T09:22:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=493)
[2026-06-08T09:22:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=489)
[2026-06-08T09:22:40] Searching for fusions with >=4 spliced events (remaining=498)
[2026-06-08T09:22:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=146)
[2026-06-08T09:22:58] Filtering fusions with anchors <=23nt (remaining=105)
[2026-06-08T09:22:58] Filtering end-to-end fusions with low support (remaining=99)
[2026-06-08T09:22:59] Filtering fusions with no coverage around the breakpoints (remaining=98)
[2026-06-08T09:22:59] Indexing gene sequences 
[2026-06-08T09:23:00] Filtering genes with >=30% identity (remaining=56)
[2026-06-08T09:23:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=10)
[2026-06-08T09:23:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=9)
[2026-06-08T09:23:02] Searching for additional isoforms (remaining=15)
[2026-06-08T09:23:03] Assigning confidence scores to events 
[2026-06-08T09:23:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:23:05] Writing fusions to file 'ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:23:06] Writing discarded fusions to file 'ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:23:21] Freeing resources
[2026-06-08T09:23:59] Done (elapsed time=00:17:00, CPU time=00:16:57, peak memory=34.2gb)