[2026-05-28T21:03:23] Launching Arriba 2.4.0
[2026-05-28T21:03:23] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:03:36] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:03:41] Reading chimeric alignments from 'EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=16022298)
[2026-05-28T21:10:04] Marking multi-mapping alignments (marked=12710692)
[2026-05-28T21:10:10] Detecting strandedness (reverse)
[2026-05-28T21:10:10] Assigning strands to alignments 
[2026-05-28T21:10:12] Annotating alignments 
[2026-05-28T21:11:03] Filtering duplicates (remaining=3884615)
[2026-05-28T21:11:11] 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=3258734)
[2026-05-28T21:11:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3258734)
[2026-05-28T21:11:16] Filtering viral contigs with expression lower than the top 5 (remaining=3258734)
[2026-05-28T21:11:22] Filtering viral contigs with less than 5% coverage (remaining=3258734)
[2026-05-28T21:11:25] Estimating fragment length (mate gap mean=-68.8138, mate gap stddev=28.1356, read length mean=103.131)
[2026-05-28T21:11:25] Filtering read-through fragments with a distance <=10000bp (remaining=3199548)
[2026-05-28T21:11:28] Filtering inconsistently clipped mates (remaining=3117936)
[2026-05-28T21:11:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2685252)
[2026-05-28T21:11:35] Filtering fragments with small insert size (remaining=2682675)
[2026-05-28T21:11:37] Filtering alignments with long gaps (remaining=2682675)
[2026-05-28T21:11:40] Filtering fragments with both mates in the same gene (remaining=2681435)
[2026-05-28T21:11:43] Filtering fusions arising from hairpin structures (remaining=2560691)
[2026-05-28T21:11:46] Filtering reads with a mismatch p-value <=0.01 (remaining=701670)
[2026-05-28T21:11:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=287242)
[2026-05-28T21:12:00] Finding fusions and counting supporting reads (total=283325)
[2026-05-28T21:12:19] Merging adjacent fusion breakpoints (remaining=282067)
[2026-05-28T21:12:20] Filtering multi-mapping fusions by alignment score and read support (remaining=108294)
[2026-05-28T21:13:02] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:13:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=106436)
[2026-05-28T21:13:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=89593)
[2026-05-28T21:13:08] Filtering fusions with <2 supporting reads (remaining=3016)
[2026-05-28T21:13:08] Filtering fusions with an e-value >=0.3 (remaining=624)
[2026-05-28T21:13:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=627)
[2026-05-28T21:13:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=498)
[2026-05-28T21:13:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=498)
[2026-05-28T21:13:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=498)
[2026-05-28T21:13:20] Searching for fusions with spliced split reads (remaining=536)
[2026-05-28T21:13:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=435)
[2026-05-28T21:13:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=433)
[2026-05-28T21:13:27] Searching for fusions with >=4 spliced events (remaining=498)
[2026-05-28T21:13:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=179)
[2026-05-28T21:13:45] Filtering fusions with anchors <=23nt (remaining=164)
[2026-05-28T21:13:46] Filtering end-to-end fusions with low support (remaining=159)
[2026-05-28T21:13:46] Filtering fusions with no coverage around the breakpoints (remaining=156)
[2026-05-28T21:13:47] Indexing gene sequences 
[2026-05-28T21:13:48] Filtering genes with >=30% identity (remaining=88)
[2026-05-28T21:13:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=55)
[2026-05-28T21:13:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=36)
[2026-05-28T21:13:51] Searching for additional isoforms (remaining=37)
[2026-05-28T21:13:52] Assigning confidence scores to events 
[2026-05-28T21:13:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:13:55] Writing fusions to file 'EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:13:55] Writing discarded fusions to file 'EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:14:16] Freeing resources
[2026-05-28T21:14:38] Done (elapsed time=00:11:15, CPU time=00:11:14, peak memory=20.5gb)