[2026-06-08T08:43:18] Launching Arriba 2.4.0
[2026-06-08T08:43:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:27] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:31] Reading chimeric alignments from 'PX_FFPE_pan_TRNA_nat_02_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=15523218)
[2026-06-08T08:49:52] Marking multi-mapping alignments (marked=10797776)
[2026-06-08T08:49:58] Detecting strandedness (reverse)
[2026-06-08T08:49:58] Assigning strands to alignments 
[2026-06-08T08:50:01] Annotating alignments 
[2026-06-08T08:50:48] Filtering duplicates (remaining=3910678)
[2026-06-08T08:50:56] 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=3515158)
[2026-06-08T08:51:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3515158)
[2026-06-08T08:51:03] Filtering viral contigs with expression lower than the top 5 (remaining=3515158)
[2026-06-08T08:51:09] Filtering viral contigs with less than 5% coverage (remaining=3515158)
[2026-06-08T08:51:13] Estimating fragment length (mate gap mean=-85.1471, mate gap stddev=27.917, read length mean=120.033)
[2026-06-08T08:51:13] Filtering read-through fragments with a distance <=10000bp (remaining=3268652)
[2026-06-08T08:51:16] Filtering inconsistently clipped mates (remaining=3202085)
[2026-06-08T08:51:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2984233)
[2026-06-08T08:51:23] Filtering fragments with small insert size (remaining=2982873)
[2026-06-08T08:51:26] Filtering alignments with long gaps (remaining=2982873)
[2026-06-08T08:51:30] Filtering fragments with both mates in the same gene (remaining=2982249)
[2026-06-08T08:51:33] Filtering fusions arising from hairpin structures (remaining=2862458)
[2026-06-08T08:51:36] Filtering reads with a mismatch p-value <=0.01 (remaining=1090921)
[2026-06-08T08:51:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=455613)
[2026-06-08T08:51:55] Finding fusions and counting supporting reads (total=349157)
[2026-06-08T08:52:14] Merging adjacent fusion breakpoints (remaining=344092)
[2026-06-08T08:52:15] Filtering multi-mapping fusions by alignment score and read support (remaining=176632)
[2026-06-08T08:53:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=175807)
[2026-06-08T08:53:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=114213)
[2026-06-08T08:53:10] Filtering fusions with <2 supporting reads (remaining=15093)
[2026-06-08T08:53:11] Filtering fusions with an e-value >=0.3 (remaining=3548)
[2026-06-08T08:53:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3577)
[2026-06-08T08:53:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3516)
[2026-06-08T08:53:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3516)
[2026-06-08T08:53:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2098)
[2026-06-08T08:53:22] Searching for fusions with spliced split reads (remaining=2147)
[2026-06-08T08:53:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=1513)
[2026-06-08T08:53:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1504)
[2026-06-08T08:53:29] Searching for fusions with >=4 spliced events (remaining=1721)
[2026-06-08T08:53:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=559)
[2026-06-08T08:53:42] Filtering fusions with anchors <=23nt (remaining=469)
[2026-06-08T08:53:43] Filtering end-to-end fusions with low support (remaining=458)
[2026-06-08T08:53:43] Filtering fusions with no coverage around the breakpoints (remaining=443)
[2026-06-08T08:53:44] Indexing gene sequences 
[2026-06-08T08:53:45] Filtering genes with >=30% identity (remaining=135)
[2026-06-08T08:53:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=60)
[2026-06-08T08:53:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=57)
[2026-06-08T08:53:48] Searching for additional isoforms (remaining=64)
[2026-06-08T08:53:49] Assigning confidence scores to events 
[2026-06-08T08:53:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:51] Writing fusions to file 'PX_FFPE_pan_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:51] Writing discarded fusions to file 'PX_FFPE_pan_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:10] Freeing resources
[2026-06-08T08:54:34] Done (elapsed time=00:11:16, CPU time=00:11:15, peak memory=19.7gb)