[2026-05-28T20:39:31] Launching Arriba 2.4.0
[2026-05-28T20:39:31] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:39:45] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:39:50] Reading chimeric alignments from 'ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=7598485)
[2026-05-28T20:43:29] Marking multi-mapping alignments (marked=5738921)
[2026-05-28T20:43:32] Detecting strandedness (reverse)
[2026-05-28T20:43:32] Assigning strands to alignments 
[2026-05-28T20:43:33] Annotating alignments 
[2026-05-28T20:43:58] Filtering duplicates (remaining=1823207)
[2026-05-28T20:44:02] 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=1612371)
[2026-05-28T20:44:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1612371)
[2026-05-28T20:44:05] Filtering viral contigs with expression lower than the top 5 (remaining=1612371)
[2026-05-28T20:44:07] Filtering viral contigs with less than 5% coverage (remaining=1612371)
[2026-05-28T20:44:09] Estimating fragment length (mate gap mean=-65.7286, mate gap stddev=30.1351, read length mean=100.55)
[2026-05-28T20:44:09] Filtering read-through fragments with a distance <=10000bp (remaining=1579223)
[2026-05-28T20:44:10] Filtering inconsistently clipped mates (remaining=1533039)
[2026-05-28T20:44:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1354393)
[2026-05-28T20:44:14] Filtering fragments with small insert size (remaining=1353278)
[2026-05-28T20:44:15] Filtering alignments with long gaps (remaining=1353278)
[2026-05-28T20:44:16] Filtering fragments with both mates in the same gene (remaining=1352372)
[2026-05-28T20:44:18] Filtering fusions arising from hairpin structures (remaining=1285368)
[2026-05-28T20:44:19] Filtering reads with a mismatch p-value <=0.01 (remaining=296708)
[2026-05-28T20:44:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=111633)
[2026-05-28T20:44:26] Finding fusions and counting supporting reads (total=118137)
[2026-05-28T20:44:35] Merging adjacent fusion breakpoints (remaining=117755)
[2026-05-28T20:44:36] Filtering multi-mapping fusions by alignment score and read support (remaining=47250)
[2026-05-28T20:44:58] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:45:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=46530)
[2026-05-28T20:45:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=38148)
[2026-05-28T20:45:02] Filtering fusions with <2 supporting reads (remaining=956)
[2026-05-28T20:45:02] Filtering fusions with an e-value >=0.3 (remaining=291)
[2026-05-28T20:45:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=291)
[2026-05-28T20:45:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=248)
[2026-05-28T20:45:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=248)
[2026-05-28T20:45:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=235)
[2026-05-28T20:45:08] Searching for fusions with spliced split reads (remaining=254)
[2026-05-28T20:45:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=202)
[2026-05-28T20:45:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=199)
[2026-05-28T20:45:11] Searching for fusions with >=4 spliced events (remaining=210)
[2026-05-28T20:45:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=68)
[2026-05-28T20:45:27] Filtering fusions with anchors <=23nt (remaining=47)
[2026-05-28T20:45:27] Filtering end-to-end fusions with low support (remaining=43)
[2026-05-28T20:45:28] Filtering fusions with no coverage around the breakpoints (remaining=43)
[2026-05-28T20:45:28] Indexing gene sequences 
[2026-05-28T20:45:29] Filtering genes with >=30% identity (remaining=10)
[2026-05-28T20:45:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-05-28T20:45:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-05-28T20:45:30] Searching for additional isoforms (remaining=4)
[2026-05-28T20:45:31] Assigning confidence scores to events 
[2026-05-28T20:45:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:45:32] Writing fusions to file 'ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:45:33] Writing discarded fusions to file 'ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:45:46] Freeing resources
[2026-05-28T20:45:58] Done (elapsed time=00:06:27, CPU time=00:06:26, peak memory=11.8gb)