[2026-05-28T21:21:35] Launching Arriba 2.4.0
[2026-05-28T21:21:35] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:21:49] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:21:54] Reading chimeric alignments from 'EndoN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=16786019)
[2026-05-28T21:32:49] Marking multi-mapping alignments (marked=12352921)
[2026-05-28T21:32:58] Detecting strandedness (no)
[2026-05-28T21:32:58] Annotating alignments 
[2026-05-28T21:34:36] Filtering duplicates (remaining=4908197)
[2026-05-28T21:34:52] 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=4416018)
[2026-05-28T21:34:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4416018)
[2026-05-28T21:35:00] Filtering viral contigs with expression lower than the top 5 (remaining=4416018)
[2026-05-28T21:35:08] Filtering viral contigs with less than 5% coverage (remaining=4416018)
[2026-05-28T21:35:12] Estimating fragment length (mate gap mean=-74.3899, mate gap stddev=29.0761, read length mean=109.585)
[2026-05-28T21:35:12] Filtering read-through fragments with a distance <=10000bp (remaining=4320600)
[2026-05-28T21:35:17] Filtering inconsistently clipped mates (remaining=4209406)
[2026-05-28T21:35:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3769061)
[2026-05-28T21:35:27] Filtering fragments with small insert size (remaining=3766675)
[2026-05-28T21:35:32] Filtering alignments with long gaps (remaining=3766675)
[2026-05-28T21:35:36] Filtering fragments with both mates in the same gene (remaining=3764827)
[2026-05-28T21:35:41] Filtering fusions arising from hairpin structures (remaining=3575177)
[2026-05-28T21:35:45] Filtering reads with a mismatch p-value <=0.01 (remaining=1121908)
[2026-05-28T21:36:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=408578)
[2026-05-28T21:36:14] Finding fusions and counting supporting reads (total=389324)
[2026-05-28T21:36:43] Merging adjacent fusion breakpoints (remaining=386892)
[2026-05-28T21:36:45] Filtering multi-mapping fusions by alignment score and read support (remaining=174106)
[2026-05-28T21:37:58] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:38:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=172324)
[2026-05-28T21:38:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=130383)
[2026-05-28T21:38:12] Filtering fusions with <2 supporting reads (remaining=6952)
[2026-05-28T21:38:13] Filtering fusions with an e-value >=0.3 (remaining=1439)
[2026-05-28T21:38:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1458)
[2026-05-28T21:38:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1344)
[2026-05-28T21:38:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1344)
[2026-05-28T21:38:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1343)
[2026-05-28T21:38:35] Searching for fusions with spliced split reads (remaining=1435)
[2026-05-28T21:38:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=1127)
[2026-05-28T21:38:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1108)
[2026-05-28T21:38:51] Searching for fusions with >=4 spliced events (remaining=1216)
[2026-05-28T21:38:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=401)
[2026-05-28T21:39:20] Filtering fusions with anchors <=23nt (remaining=357)
[2026-05-28T21:39:21] Filtering end-to-end fusions with low support (remaining=343)
[2026-05-28T21:39:22] Filtering fusions with no coverage around the breakpoints (remaining=339)
[2026-05-28T21:39:23] Indexing gene sequences 
[2026-05-28T21:39:28] Filtering genes with >=30% identity (remaining=145)
[2026-05-28T21:39:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=79)
[2026-05-28T21:39:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=76)
[2026-05-28T21:39:33] Searching for additional isoforms (remaining=78)
[2026-05-28T21:39:35] Assigning confidence scores to events 
[2026-05-28T21:39:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:39:40] Writing fusions to file 'EndoN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:39:41] Writing discarded fusions to file 'EndoN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'