[2026-06-08T08:37:24] Launching Arriba 2.4.0
[2026-06-08T08:37:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:41] Reading chimeric alignments from 'PX_FFPE_pst_TRNA_nat_02_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=11992623)
[2026-06-08T08:44:05] Marking multi-mapping alignments (marked=7560604)
[2026-06-08T08:44:10] Detecting strandedness (reverse)
[2026-06-08T08:44:10] Assigning strands to alignments 
[2026-06-08T08:44:12] Annotating alignments 
[2026-06-08T08:44:51] Filtering duplicates (remaining=4559431)
[2026-06-08T08:44:57] 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=4356297)
[2026-06-08T08:45:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4356297)
[2026-06-08T08:45:02] Filtering viral contigs with expression lower than the top 5 (remaining=4356297)
[2026-06-08T08:45:07] Filtering viral contigs with less than 5% coverage (remaining=4356297)
[2026-06-08T08:45:10] Estimating fragment length (mate gap mean=-87.4652, mate gap stddev=26.6115, read length mean=126.193)
[2026-06-08T08:45:10] Filtering read-through fragments with a distance <=10000bp (remaining=4100300)
[2026-06-08T08:45:12] Filtering inconsistently clipped mates (remaining=4028550)
[2026-06-08T08:45:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3878090)
[2026-06-08T08:45:18] Filtering fragments with small insert size (remaining=3877046)
[2026-06-08T08:45:21] Filtering alignments with long gaps (remaining=3877046)
[2026-06-08T08:45:23] Filtering fragments with both mates in the same gene (remaining=3876297)
[2026-06-08T08:45:25] Filtering fusions arising from hairpin structures (remaining=3691303)
[2026-06-08T08:45:28] Filtering reads with a mismatch p-value <=0.01 (remaining=1689899)
[2026-06-08T08:45:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=598865)
[2026-06-08T08:45:48] Finding fusions and counting supporting reads (total=509721)
[2026-06-08T08:46:04] Merging adjacent fusion breakpoints (remaining=506258)
[2026-06-08T08:46:05] Filtering multi-mapping fusions by alignment score and read support (remaining=291598)
[2026-06-08T08:46:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=290484)
[2026-06-08T08:46:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=166124)
[2026-06-08T08:46:48] Filtering fusions with <2 supporting reads (remaining=18055)
[2026-06-08T08:46:48] Filtering fusions with an e-value >=0.3 (remaining=4107)
[2026-06-08T08:46:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4144)
[2026-06-08T08:46:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4068)
[2026-06-08T08:46:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4068)
[2026-06-08T08:46:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4008)
[2026-06-08T08:46:58] Searching for fusions with spliced split reads (remaining=4065)
[2026-06-08T08:47:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=2844)
[2026-06-08T08:47:04] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2813)
[2026-06-08T08:47:05] Searching for fusions with >=4 spliced events (remaining=3257)
[2026-06-08T08:47:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1037)
[2026-06-08T08:47:20] Filtering fusions with anchors <=23nt (remaining=917)
[2026-06-08T08:47:20] Filtering end-to-end fusions with low support (remaining=892)
[2026-06-08T08:47:21] Filtering fusions with no coverage around the breakpoints (remaining=873)
[2026-06-08T08:47:21] Indexing gene sequences 
[2026-06-08T08:47:25] Filtering genes with >=30% identity (remaining=259)
[2026-06-08T08:47:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=115)
[2026-06-08T08:47:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=115)
[2026-06-08T08:47:30] Searching for additional isoforms (remaining=133)
[2026-06-08T08:47:31] Assigning confidence scores to events 
[2026-06-08T08:47:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:33] Writing fusions to file 'PX_FFPE_pst_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:34] Writing discarded fusions to file 'PX_FFPE_pst_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:57] Freeing resources
[2026-06-08T08:48:16] Done (elapsed time=00:10:52, CPU time=00:10:51, peak memory=16.3gb)