[2026-06-08T08:32:11] Launching Arriba 2.4.0
[2026-06-08T08:32:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:24] Reading chimeric alignments from 'PX_FFPE_stm_TRNA_nat_02_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=8266590)
[2026-06-08T08:37:06] Marking multi-mapping alignments (marked=5326887)
[2026-06-08T08:37:11] Detecting strandedness (reverse)
[2026-06-08T08:37:11] Assigning strands to alignments 
[2026-06-08T08:37:13] Annotating alignments 
[2026-06-08T08:37:49] Filtering duplicates (remaining=4155667)
[2026-06-08T08:37:57] 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=3908737)
[2026-06-08T08:37:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3908737)
[2026-06-08T08:38:02] Filtering viral contigs with expression lower than the top 5 (remaining=3908737)
[2026-06-08T08:38:07] Filtering viral contigs with less than 5% coverage (remaining=3908737)
[2026-06-08T08:38:10] Estimating fragment length (mate gap mean=-90.2402, mate gap stddev=28.8712, read length mean=134.828)
[2026-06-08T08:38:10] Filtering read-through fragments with a distance <=10000bp (remaining=3677462)
[2026-06-08T08:38:13] Filtering inconsistently clipped mates (remaining=3618959)
[2026-06-08T08:38:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3530147)
[2026-06-08T08:38:20] Filtering fragments with small insert size (remaining=3529581)
[2026-06-08T08:38:22] Filtering alignments with long gaps (remaining=3529581)
[2026-06-08T08:38:25] Filtering fragments with both mates in the same gene (remaining=3529079)
[2026-06-08T08:38:27] Filtering fusions arising from hairpin structures (remaining=3344948)
[2026-06-08T08:38:31] Filtering reads with a mismatch p-value <=0.01 (remaining=1669398)
[2026-06-08T08:38:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=599838)
[2026-06-08T08:38:51] Finding fusions and counting supporting reads (total=447792)
[2026-06-08T08:39:14] Merging adjacent fusion breakpoints (remaining=443804)
[2026-06-08T08:39:15] Filtering multi-mapping fusions by alignment score and read support (remaining=280397)
[2026-06-08T08:39:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=278926)
[2026-06-08T08:40:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=164374)
[2026-06-08T08:40:01] Filtering fusions with <2 supporting reads (remaining=44483)
[2026-06-08T08:40:02] Filtering fusions with an e-value >=0.3 (remaining=26162)
[2026-06-08T08:40:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=26196)
[2026-06-08T08:40:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=26154)
[2026-06-08T08:40:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=26154)
[2026-06-08T08:40:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4810)
[2026-06-08T08:40:14] Searching for fusions with spliced split reads (remaining=4911)
[2026-06-08T08:40:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=3229)
[2026-06-08T08:40:21] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3201)
[2026-06-08T08:40:21] Searching for fusions with >=4 spliced events (remaining=3575)
[2026-06-08T08:40:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=943)
[2026-06-08T08:40:40] Filtering fusions with anchors <=23nt (remaining=768)
[2026-06-08T08:40:41] Filtering end-to-end fusions with low support (remaining=751)
[2026-06-08T08:40:42] Filtering fusions with no coverage around the breakpoints (remaining=734)
[2026-06-08T08:40:42] Indexing gene sequences 
[2026-06-08T08:40:48] Filtering genes with >=30% identity (remaining=224)
[2026-06-08T08:40:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=122)
[2026-06-08T08:40:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=121)
[2026-06-08T08:40:53] Searching for additional isoforms (remaining=139)
[2026-06-08T08:40:55] Assigning confidence scores to events 
[2026-06-08T08:40:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:57] Writing fusions to file 'PX_FFPE_stm_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:40:59] Writing discarded fusions to file 'PX_FFPE_stm_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:29] Freeing resources
[2026-06-08T08:41:50] Done (elapsed time=00:09:39, CPU time=00:09:37, peak memory=12.6gb)