[2026-06-08T08:26:53] Launching Arriba 2.4.0
[2026-06-08T08:26:53] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:07] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:12] Reading chimeric alignments from 'EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=16023386)
[2026-06-08T08:36:44] Marking multi-mapping alignments (marked=11773801)
[2026-06-08T08:36:50] Detecting strandedness (reverse)
[2026-06-08T08:36:50] Assigning strands to alignments 
[2026-06-08T08:36:53] Annotating alignments 
[2026-06-08T08:37:48] Filtering duplicates (remaining=4635904)
[2026-06-08T08:37:56] 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)
[2026-06-08T08:37:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4125346)
[2026-06-08T08:38:02] Filtering viral contigs with expression lower than the top 5 (remaining=4125346)
[2026-06-08T08:38:09] Filtering viral contigs with less than 5% coverage (remaining=4125346)
[2026-06-08T08:38:13] Estimating fragment length (mate gap mean=-74.8598, mate gap stddev=29.0913, read length mean=110.757)
[2026-06-08T08:38:13] Filtering read-through fragments with a distance <=10000bp (remaining=4027701)
[2026-06-08T08:38:16] Filtering inconsistently clipped mates (remaining=3917443)
[2026-06-08T08:38:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3555494)
[2026-06-08T08:38:24] Filtering fragments with small insert size (remaining=3552848)
[2026-06-08T08:38:27] Filtering alignments with long gaps (remaining=3552848)
[2026-06-08T08:38:30] Filtering fragments with both mates in the same gene (remaining=3551199)
[2026-06-08T08:38:34] Filtering fusions arising from hairpin structures (remaining=3369108)
[2026-06-08T08:38:37] Filtering reads with a mismatch p-value <=0.01 (remaining=1101836)
[2026-06-08T08:38:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=379442)
[2026-06-08T08:38:55] Finding fusions and counting supporting reads (total=349548)
[2026-06-08T08:39:17] Merging adjacent fusion breakpoints (remaining=347278)
[2026-06-08T08:39:19] Filtering multi-mapping fusions by alignment score and read support (remaining=165318)
[2026-06-08T08:40:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=163997)
[2026-06-08T08:40:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=115933)
[2026-06-08T08:40:21] Filtering fusions with <2 supporting reads (remaining=7454)
[2026-06-08T08:40:21] Filtering fusions with an e-value >=0.3 (remaining=1658)
[2026-06-08T08:40:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1680)
[2026-06-08T08:40:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1568)
[2026-06-08T08:40:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1568)
[2026-06-08T08:40:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1556)
[2026-06-08T08:40:35] Searching for fusions with spliced split reads (remaining=1631)
[2026-06-08T08:40:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=1288)
[2026-06-08T08:40:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1275)
[2026-06-08T08:40:43] Searching for fusions with >=4 spliced events (remaining=1381)
[2026-06-08T08:40:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=408)
[2026-06-08T08:41:10] Filtering fusions with anchors <=23nt (remaining=352)
[2026-06-08T08:41:11] Filtering end-to-end fusions with low support (remaining=345)
[2026-06-08T08:41:11] Filtering fusions with no coverage around the breakpoints (remaining=335)
[2026-06-08T08:41:12] Indexing gene sequences 
[2026-06-08T08:41:15] Filtering genes with >=30% identity (remaining=148)
[2026-06-08T08:41:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=80)
[2026-06-08T08:41:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=70)
[2026-06-08T08:41:18] Searching for additional isoforms (remaining=76)
[2026-06-08T08:41:19] Assigning confidence scores to events 
[2026-06-08T08:41:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:22] Writing fusions to file 'EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:22] Writing discarded fusions to file 'EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:51] Freeing resources
[2026-06-08T08:42:19] Done (elapsed time=00:15:26, CPU time=00:15:26, peak memory=20.5gb)