[2026-05-28T21:14:32] Launching Arriba 2.4.0
[2026-05-28T21:14:32] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:14:47] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:14:51] Reading chimeric alignments from 'EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=16023386)
[2026-05-28T21:22:51] Marking multi-mapping alignments (marked=11773801)
[2026-05-28T21:22:57] Detecting strandedness (reverse)
[2026-05-28T21:22:57] Assigning strands to alignments 
[2026-05-28T21:23:00] Annotating alignments 
[2026-05-28T21:23:51] Filtering duplicates (remaining=4635904)
[2026-05-28T21:23:58] 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=4125346)
[2026-05-28T21:24:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4125346)
[2026-05-28T21:24:04] Filtering viral contigs with expression lower than the top 5 (remaining=4125346)
[2026-05-28T21:24:10] Filtering viral contigs with less than 5% coverage (remaining=4125346)
[2026-05-28T21:24:13] Estimating fragment length (mate gap mean=-74.8598, mate gap stddev=29.0913, read length mean=110.757)
[2026-05-28T21:24:13] Filtering read-through fragments with a distance <=10000bp (remaining=4027701)
[2026-05-28T21:24:16] Filtering inconsistently clipped mates (remaining=3917443)
[2026-05-28T21:24:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3555494)
[2026-05-28T21:24:23] Filtering fragments with small insert size (remaining=3552848)
[2026-05-28T21:24:26] Filtering alignments with long gaps (remaining=3552848)
[2026-05-28T21:24:29] Filtering fragments with both mates in the same gene (remaining=3551199)
[2026-05-28T21:24:32] Filtering fusions arising from hairpin structures (remaining=3369108)
[2026-05-28T21:24:35] Filtering reads with a mismatch p-value <=0.01 (remaining=1101836)
[2026-05-28T21:24:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=379442)
[2026-05-28T21:24:54] Finding fusions and counting supporting reads (total=349548)
[2026-05-28T21:25:15] Merging adjacent fusion breakpoints (remaining=347278)
[2026-05-28T21:25:17] Filtering multi-mapping fusions by alignment score and read support (remaining=165318)
[2026-05-28T21:26:03] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:26:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=163997)
[2026-05-28T21:26:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=115933)
[2026-05-28T21:26:10] Filtering fusions with <2 supporting reads (remaining=7454)
[2026-05-28T21:26:10] Filtering fusions with an e-value >=0.3 (remaining=1658)
[2026-05-28T21:26:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1680)
[2026-05-28T21:26:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1568)
[2026-05-28T21:26:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1568)
[2026-05-28T21:26:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1556)
[2026-05-28T21:26:22] Searching for fusions with spliced split reads (remaining=1631)
[2026-05-28T21:26:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=1288)
[2026-05-28T21:26:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1275)
[2026-05-28T21:26:30] Searching for fusions with >=4 spliced events (remaining=1381)
[2026-05-28T21:26:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=408)
[2026-05-28T21:26:46] Filtering fusions with anchors <=23nt (remaining=352)
[2026-05-28T21:26:46] Filtering end-to-end fusions with low support (remaining=345)
[2026-05-28T21:26:47] Filtering fusions with no coverage around the breakpoints (remaining=335)
[2026-05-28T21:26:48] Indexing gene sequences 
[2026-05-28T21:26:50] Filtering genes with >=30% identity (remaining=148)
[2026-05-28T21:26:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=80)
[2026-05-28T21:26:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=70)
[2026-05-28T21:26:54] Searching for additional isoforms (remaining=76)
[2026-05-28T21:26:55] Assigning confidence scores to events 
[2026-05-28T21:26:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:26:59] Writing fusions to file 'EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:27:00] Writing discarded fusions to file 'EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:27:34] Freeing resources
[2026-05-28T21:28:06] Done (elapsed time=00:13:34, CPU time=00:13:33, peak memory=20.5gb)