[2026-06-08T08:59:32] Launching Arriba 2.4.0
[2026-06-08T08:59:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:59:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:59:44] Reading chimeric alignments from 'PX_FFPE_stm_TRNA_nat_01_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=14473184)
[2026-06-08T09:07:23] Marking multi-mapping alignments (marked=9230359)
[2026-06-08T09:07:29] Detecting strandedness (reverse)
[2026-06-08T09:07:29] Assigning strands to alignments 
[2026-06-08T09:07:32] Annotating alignments 
[2026-06-08T09:08:20] Filtering duplicates (remaining=5765215)
[2026-06-08T09:08:29] 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=5442336)
[2026-06-08T09:08:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5442336)
[2026-06-08T09:08:35] Filtering viral contigs with expression lower than the top 5 (remaining=5442336)
[2026-06-08T09:08:41] Filtering viral contigs with less than 5% coverage (remaining=5442336)
[2026-06-08T09:08:45] Estimating fragment length (mate gap mean=-91.1425, mate gap stddev=28.0646, read length mean=132.711)
[2026-06-08T09:08:45] Filtering read-through fragments with a distance <=10000bp (remaining=5098609)
[2026-06-08T09:08:48] Filtering inconsistently clipped mates (remaining=5009879)
[2026-06-08T09:08:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4858039)
[2026-06-08T09:08:56] Filtering fragments with small insert size (remaining=4857051)
[2026-06-08T09:08:58] Filtering alignments with long gaps (remaining=4857051)
[2026-06-08T09:09:01] Filtering fragments with both mates in the same gene (remaining=4856320)
[2026-06-08T09:09:04] Filtering fusions arising from hairpin structures (remaining=4608485)
[2026-06-08T09:09:08] Filtering reads with a mismatch p-value <=0.01 (remaining=2185081)
[2026-06-08T09:09:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=812790)
[2026-06-08T09:09:32] Finding fusions and counting supporting reads (total=611391)
[2026-06-08T09:09:53] Merging adjacent fusion breakpoints (remaining=604997)
[2026-06-08T09:09:55] Filtering multi-mapping fusions by alignment score and read support (remaining=359396)
[2026-06-08T09:10:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:10:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=357777)
[2026-06-08T09:10:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=208896)
[2026-06-08T09:10:50] Filtering fusions with <2 supporting reads (remaining=45224)
[2026-06-08T09:10:50] Filtering fusions with an e-value >=0.3 (remaining=21703)
[2026-06-08T09:10:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=21755)
[2026-06-08T09:10:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=21693)
[2026-06-08T09:10:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=21693)
[2026-06-08T09:10:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5513)
[2026-06-08T09:11:04] Searching for fusions with spliced split reads (remaining=5632)
[2026-06-08T09:11:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=3757)
[2026-06-08T09:11:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3721)
[2026-06-08T09:11:11] Searching for fusions with >=4 spliced events (remaining=4263)
[2026-06-08T09:11:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1318)
[2026-06-08T09:11:27] Filtering fusions with anchors <=23nt (remaining=1086)
[2026-06-08T09:11:27] Filtering end-to-end fusions with low support (remaining=1059)
[2026-06-08T09:11:28] Filtering fusions with no coverage around the breakpoints (remaining=1031)
[2026-06-08T09:11:28] Indexing gene sequences 
[2026-06-08T09:11:33] Filtering genes with >=30% identity (remaining=315)
[2026-06-08T09:11:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=133)
[2026-06-08T09:11:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=127)
[2026-06-08T09:11:38] Searching for additional isoforms (remaining=151)
[2026-06-08T09:11:39] Assigning confidence scores to events 
[2026-06-08T09:11:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:11:42] Writing fusions to file 'PX_FFPE_stm_TRNA_nat_01_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:11:43] Writing discarded fusions to file 'PX_FFPE_stm_TRNA_nat_01_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:12:09] Freeing resources
[2026-06-08T09:12:32] Done (elapsed time=00:13:00, CPU time=00:12:58, peak memory=18.9gb)