[2026-06-08T07:56:31] Launching Arriba 2.4.0
[2026-06-08T07:56:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:56:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:56:56] Reading chimeric alignments from 'ColoN_FFPE_L06_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=11404607)
[2026-06-08T08:02:04] Marking multi-mapping alignments (marked=9153790)
[2026-06-08T08:02:09] Detecting strandedness (no)
[2026-06-08T08:02:09] Annotating alignments 
[2026-06-08T08:02:53] Filtering duplicates (remaining=1911061)
[2026-06-08T08:03:00] 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=1525308)
[2026-06-08T08:03:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1525308)
[2026-06-08T08:03:04] Filtering viral contigs with expression lower than the top 5 (remaining=1525308)
[2026-06-08T08:03:09] Filtering viral contigs with less than 5% coverage (remaining=1525308)
[2026-06-08T08:03:11] Estimating fragment length (mate gap mean=-65.2715, mate gap stddev=29.5974, read length mean=98.6059)
[2026-06-08T08:03:11] Filtering read-through fragments with a distance <=10000bp (remaining=1484929)
[2026-06-08T08:03:14] Filtering inconsistently clipped mates (remaining=1431424)
[2026-06-08T08:03:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1317012)
[2026-06-08T08:03:19] Filtering fragments with small insert size (remaining=1315301)
[2026-06-08T08:03:21] Filtering alignments with long gaps (remaining=1315301)
[2026-06-08T08:03:23] Filtering fragments with both mates in the same gene (remaining=1314355)
[2026-06-08T08:03:25] Filtering fusions arising from hairpin structures (remaining=1238710)
[2026-06-08T08:03:28] Filtering reads with a mismatch p-value <=0.01 (remaining=294732)
[2026-06-08T08:03:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=91775)
[2026-06-08T08:03:37] Finding fusions and counting supporting reads (total=84153)
[2026-06-08T08:03:50] Merging adjacent fusion breakpoints (remaining=83143)
[2026-06-08T08:03:50] Filtering multi-mapping fusions by alignment score and read support (remaining=34275)
[2026-06-08T08:04:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:04:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=33656)
[2026-06-08T08:04:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=25296)
[2026-06-08T08:04:25] Filtering fusions with <2 supporting reads (remaining=1071)
[2026-06-08T08:04:25] Filtering fusions with an e-value >=0.3 (remaining=236)
[2026-06-08T08:04:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=237)
[2026-06-08T08:04:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=184)
[2026-06-08T08:04:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=184)
[2026-06-08T08:04:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=181)
[2026-06-08T08:04:33] Searching for fusions with spliced split reads (remaining=190)
[2026-06-08T08:04:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=156)
[2026-06-08T08:04:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=154)
[2026-06-08T08:04:37] Searching for fusions with >=4 spliced events (remaining=154)
[2026-06-08T08:04:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=49)
[2026-06-08T08:04:53] Filtering fusions with anchors <=23nt (remaining=40)
[2026-06-08T08:04:53] Filtering end-to-end fusions with low support (remaining=39)
[2026-06-08T08:04:53] Filtering fusions with no coverage around the breakpoints (remaining=37)
[2026-06-08T08:04:53] Indexing gene sequences 
[2026-06-08T08:04:54] Filtering genes with >=30% identity (remaining=21)
[2026-06-08T08:04:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=2)
[2026-06-08T08:04:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=2)
[2026-06-08T08:04:55] Searching for additional isoforms (remaining=2)
[2026-06-08T08:04:55] Assigning confidence scores to events 
[2026-06-08T08:04:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:04:57] Writing fusions to file 'ColoN_FFPE_L06_RNA_01_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:04:57] Writing discarded fusions to file 'ColoN_FFPE_L06_RNA_01_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:05:07] Freeing resources
[2026-06-08T08:05:26] Done (elapsed time=00:08:55, CPU time=00:08:54, peak memory=15.4gb)