[2026-06-08T08:31:06] Launching Arriba 2.4.0
[2026-06-08T08:31:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:21] Reading chimeric alignments from 'EndoN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=16786019)
[2026-06-08T08:37:43] Marking multi-mapping alignments (marked=12352921)
[2026-06-08T08:37:49] Detecting strandedness (no)
[2026-06-08T08:37:49] Annotating alignments 
[2026-06-08T08:38:39] Filtering duplicates (remaining=4908197)
[2026-06-08T08:38:45] 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)
[2026-06-08T08:38:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4416018)
[2026-06-08T08:38:51] Filtering viral contigs with expression lower than the top 5 (remaining=4416018)
[2026-06-08T08:38:57] Filtering viral contigs with less than 5% coverage (remaining=4416018)
[2026-06-08T08:39:00] Estimating fragment length (mate gap mean=-74.3899, mate gap stddev=29.0761, read length mean=109.585)
[2026-06-08T08:39:00] Filtering read-through fragments with a distance <=10000bp (remaining=4320600)
[2026-06-08T08:39:03] Filtering inconsistently clipped mates (remaining=4209406)
[2026-06-08T08:39:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3769061)
[2026-06-08T08:39:10] Filtering fragments with small insert size (remaining=3766675)
[2026-06-08T08:39:13] Filtering alignments with long gaps (remaining=3766675)
[2026-06-08T08:39:16] Filtering fragments with both mates in the same gene (remaining=3764827)
[2026-06-08T08:39:19] Filtering fusions arising from hairpin structures (remaining=3575177)
[2026-06-08T08:39:22] Filtering reads with a mismatch p-value <=0.01 (remaining=1121908)
[2026-06-08T08:39:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=408578)
[2026-06-08T08:39:38] Finding fusions and counting supporting reads (total=389324)
[2026-06-08T08:39:54] Merging adjacent fusion breakpoints (remaining=386892)
[2026-06-08T08:39:55] Filtering multi-mapping fusions by alignment score and read support (remaining=174106)
[2026-06-08T08:40:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=172324)
[2026-06-08T08:40:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=130383)
[2026-06-08T08:40:41] Filtering fusions with <2 supporting reads (remaining=6952)
[2026-06-08T08:40:42] Filtering fusions with an e-value >=0.3 (remaining=1439)
[2026-06-08T08:40:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1458)
[2026-06-08T08:40:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1344)
[2026-06-08T08:40:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1344)
[2026-06-08T08:40:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1343)
[2026-06-08T08:40:54] Searching for fusions with spliced split reads (remaining=1435)
[2026-06-08T08:41:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=1127)
[2026-06-08T08:41:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1108)
[2026-06-08T08:41:01] Searching for fusions with >=4 spliced events (remaining=1216)
[2026-06-08T08:41:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=401)
[2026-06-08T08:41:15] Filtering fusions with anchors <=23nt (remaining=357)
[2026-06-08T08:41:15] Filtering end-to-end fusions with low support (remaining=343)
[2026-06-08T08:41:16] Filtering fusions with no coverage around the breakpoints (remaining=339)
[2026-06-08T08:41:16] Indexing gene sequences 
[2026-06-08T08:41:19] Filtering genes with >=30% identity (remaining=145)
[2026-06-08T08:41:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=79)
[2026-06-08T08:41:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=76)
[2026-06-08T08:41:22] Searching for additional isoforms (remaining=78)
[2026-06-08T08:41:23] Assigning confidence scores to events 
[2026-06-08T08:41:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:26] Writing fusions to file 'EndoN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:26] Writing discarded fusions to file 'EndoN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:44] Freeing resources
[2026-06-08T08:42:05] Done (elapsed time=00:10:59, CPU time=00:10:58, peak memory=21.3gb)