[2026-06-08T08:39:28] Launching Arriba 2.4.0
[2026-06-08T08:39:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:40] Reading chimeric alignments from 'PX_FFPE_kid_TRNA_nat_02_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=14636614)
[2026-06-08T08:46:05] Marking multi-mapping alignments (marked=9938175)
[2026-06-08T08:46:11] Detecting strandedness (reverse)
[2026-06-08T08:46:11] Assigning strands to alignments 
[2026-06-08T08:46:13] Annotating alignments 
[2026-06-08T08:47:02] Filtering duplicates (remaining=3960160)
[2026-06-08T08:47:09] 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=3516573)
[2026-06-08T08:47:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3516573)
[2026-06-08T08:47:15] Filtering viral contigs with expression lower than the top 5 (remaining=3516573)
[2026-06-08T08:47:21] Filtering viral contigs with less than 5% coverage (remaining=3516573)
[2026-06-08T08:47:24] Estimating fragment length (mate gap mean=-84.6368, mate gap stddev=28.0216, read length mean=122.374)
[2026-06-08T08:47:24] Filtering read-through fragments with a distance <=10000bp (remaining=3370721)
[2026-06-08T08:47:27] Filtering inconsistently clipped mates (remaining=3302270)
[2026-06-08T08:47:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3131043)
[2026-06-08T08:47:34] Filtering fragments with small insert size (remaining=3129560)
[2026-06-08T08:47:37] Filtering alignments with long gaps (remaining=3129560)
[2026-06-08T08:47:40] Filtering fragments with both mates in the same gene (remaining=3128830)
[2026-06-08T08:47:43] Filtering fusions arising from hairpin structures (remaining=2990797)
[2026-06-08T08:47:46] Filtering reads with a mismatch p-value <=0.01 (remaining=1213893)
[2026-06-08T08:47:55] Filtering reads with low entropy (k-mer content >=60%) (remaining=345038)
[2026-06-08T08:48:04] Finding fusions and counting supporting reads (total=308996)
[2026-06-08T08:48:22] Merging adjacent fusion breakpoints (remaining=307265)
[2026-06-08T08:48:23] Filtering multi-mapping fusions by alignment score and read support (remaining=160874)
[2026-06-08T08:49:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=159658)
[2026-06-08T08:49:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=99936)
[2026-06-08T08:49:15] Filtering fusions with <2 supporting reads (remaining=7290)
[2026-06-08T08:49:15] Filtering fusions with an e-value >=0.3 (remaining=1790)
[2026-06-08T08:49:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1812)
[2026-06-08T08:49:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1733)
[2026-06-08T08:49:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1733)
[2026-06-08T08:49:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1621)
[2026-06-08T08:49:27] Searching for fusions with spliced split reads (remaining=1723)
[2026-06-08T08:49:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=1294)
[2026-06-08T08:49:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1285)
[2026-06-08T08:49:33] Searching for fusions with >=4 spliced events (remaining=1387)
[2026-06-08T08:49:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=552)
[2026-06-08T08:49:46] Filtering fusions with anchors <=23nt (remaining=462)
[2026-06-08T08:49:47] Filtering end-to-end fusions with low support (remaining=447)
[2026-06-08T08:49:47] Filtering fusions with no coverage around the breakpoints (remaining=431)
[2026-06-08T08:49:48] Indexing gene sequences 
[2026-06-08T08:49:50] Filtering genes with >=30% identity (remaining=179)
[2026-06-08T08:49:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=85)
[2026-06-08T08:49:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=85)
[2026-06-08T08:49:53] Searching for additional isoforms (remaining=88)
[2026-06-08T08:49:54] Assigning confidence scores to events 
[2026-06-08T08:49:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:56] Writing fusions to file 'PX_FFPE_kid_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:57] Writing discarded fusions to file 'PX_FFPE_kid_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:16] Freeing resources
[2026-06-08T08:50:37] Done (elapsed time=00:11:09, CPU time=00:11:09, peak memory=18.8gb)