[2026-06-08T09:09:35] Launching Arriba 2.4.0
[2026-06-08T09:09:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:09:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:09:54] Reading chimeric alignments from 'PX_FFPE_stm_TRNA_nat_03_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=13806797)
[2026-06-08T09:18:27] Marking multi-mapping alignments (marked=8521986)
[2026-06-08T09:18:32] Detecting strandedness (reverse)
[2026-06-08T09:18:32] Assigning strands to alignments 
[2026-06-08T09:18:35] Annotating alignments 
[2026-06-08T09:19:14] Filtering duplicates (remaining=6623244)
[2026-06-08T09:19:22] 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=6373576)
[2026-06-08T09:19:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6373576)
[2026-06-08T09:19:26] Filtering viral contigs with expression lower than the top 5 (remaining=6373576)
[2026-06-08T09:19:32] Filtering viral contigs with less than 5% coverage (remaining=6373576)
[2026-06-08T09:19:34] Estimating fragment length (mate gap mean=-90.7188, mate gap stddev=27.5103, read length mean=132.397)
[2026-06-08T09:19:34] Filtering read-through fragments with a distance <=10000bp (remaining=5936679)
[2026-06-08T09:19:36] Filtering inconsistently clipped mates (remaining=5853026)
[2026-06-08T09:19:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5708725)
[2026-06-08T09:19:43] Filtering fragments with small insert size (remaining=5707767)
[2026-06-08T09:19:45] Filtering alignments with long gaps (remaining=5707767)
[2026-06-08T09:19:47] Filtering fragments with both mates in the same gene (remaining=5707023)
[2026-06-08T09:19:50] Filtering fusions arising from hairpin structures (remaining=5446683)
[2026-06-08T09:19:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2605062)
[2026-06-08T09:20:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1010593)
[2026-06-08T09:20:15] Finding fusions and counting supporting reads (total=771635)
[2026-06-08T09:20:33] Merging adjacent fusion breakpoints (remaining=764062)
[2026-06-08T09:20:34] Filtering multi-mapping fusions by alignment score and read support (remaining=475636)
[2026-06-08T09:21:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:21:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=474258)
[2026-06-08T09:21:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=264853)
[2026-06-08T09:21:19] Filtering fusions with <2 supporting reads (remaining=45389)
[2026-06-08T09:21:19] Filtering fusions with an e-value >=0.3 (remaining=15629)
[2026-06-08T09:21:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=15670)
[2026-06-08T09:21:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=15612)
[2026-06-08T09:21:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15612)
[2026-06-08T09:21:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7156)
[2026-06-08T09:21:31] Searching for fusions with spliced split reads (remaining=7283)
[2026-06-08T09:21:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=4563)
[2026-06-08T09:21:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4527)
[2026-06-08T09:21:38] Searching for fusions with >=4 spliced events (remaining=5560)
[2026-06-08T09:21:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1982)
[2026-06-08T09:21:56] Filtering fusions with anchors <=23nt (remaining=1624)
[2026-06-08T09:21:56] Filtering end-to-end fusions with low support (remaining=1591)
[2026-06-08T09:21:57] Filtering fusions with no coverage around the breakpoints (remaining=1557)
[2026-06-08T09:21:57] Indexing gene sequences 
[2026-06-08T09:22:03] Filtering genes with >=30% identity (remaining=416)
[2026-06-08T09:22:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=157)
[2026-06-08T09:22:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=146)
[2026-06-08T09:22:08] Searching for additional isoforms (remaining=173)
[2026-06-08T09:22:10] Assigning confidence scores to events 
[2026-06-08T09:22:13] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:22:13] Writing fusions to file 'PX_FFPE_stm_TRNA_nat_03_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:22:14] Writing discarded fusions to file 'PX_FFPE_stm_TRNA_nat_03_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:22:40] Freeing resources
[2026-06-08T09:22:59] Done (elapsed time=00:13:24, CPU time=00:13:23, peak memory=18.3gb)