[2026-06-08T07:56:37] Launching Arriba 2.4.0
[2026-06-08T07:56:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:56:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:56:51] Reading chimeric alignments from 'PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=6009703)
[2026-06-08T07:59:36] Marking multi-mapping alignments (marked=4000556)
[2026-06-08T07:59:39] Detecting strandedness (reverse)
[2026-06-08T07:59:39] Assigning strands to alignments 
[2026-06-08T07:59:40] Annotating alignments 
[2026-06-08T08:00:06] Filtering duplicates (remaining=1865976)
[2026-06-08T08:00:11] 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=1716024)
[2026-06-08T08:00:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1716024)
[2026-06-08T08:00:14] Filtering viral contigs with expression lower than the top 5 (remaining=1716024)
[2026-06-08T08:00:17] Filtering viral contigs with less than 5% coverage (remaining=1716024)
[2026-06-08T08:00:18] Estimating fragment length (mate gap mean=-83.0564, mate gap stddev=27.5117, read length mean=118.716)
[2026-06-08T08:00:19] Filtering read-through fragments with a distance <=10000bp (remaining=1636936)
[2026-06-08T08:00:20] Filtering inconsistently clipped mates (remaining=1601166)
[2026-06-08T08:00:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1528622)
[2026-06-08T08:00:23] Filtering fragments with small insert size (remaining=1527714)
[2026-06-08T08:00:25] Filtering alignments with long gaps (remaining=1527714)
[2026-06-08T08:00:26] Filtering fragments with both mates in the same gene (remaining=1527230)
[2026-06-08T08:00:28] Filtering fusions arising from hairpin structures (remaining=1459828)
[2026-06-08T08:00:29] Filtering reads with a mismatch p-value <=0.01 (remaining=568641)
[2026-06-08T08:00:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=186836)
[2026-06-08T08:00:39] Finding fusions and counting supporting reads (total=176412)
[2026-06-08T08:00:50] Merging adjacent fusion breakpoints (remaining=175704)
[2026-06-08T08:00:51] Filtering multi-mapping fusions by alignment score and read support (remaining=94837)
[2026-06-08T08:01:17] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:01:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=94290)
[2026-06-08T08:01:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=58381)
[2026-06-08T08:01:21] Filtering fusions with <2 supporting reads (remaining=4227)
[2026-06-08T08:01:21] Filtering fusions with an e-value >=0.3 (remaining=1050)
[2026-06-08T08:01:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1062)
[2026-06-08T08:01:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1034)
[2026-06-08T08:01:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1034)
[2026-06-08T08:01:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1033)
[2026-06-08T08:01:28] Searching for fusions with spliced split reads (remaining=1074)
[2026-06-08T08:01:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=859)
[2026-06-08T08:01:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=850)
[2026-06-08T08:01:32] Searching for fusions with >=4 spliced events (remaining=896)
[2026-06-08T08:01:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=230)
[2026-06-08T08:01:48] Filtering fusions with anchors <=23nt (remaining=196)
[2026-06-08T08:01:48] Filtering end-to-end fusions with low support (remaining=189)
[2026-06-08T08:01:48] Filtering fusions with no coverage around the breakpoints (remaining=177)
[2026-06-08T08:01:49] Indexing gene sequences 
[2026-06-08T08:01:51] Filtering genes with >=30% identity (remaining=70)
[2026-06-08T08:01:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=34)
[2026-06-08T08:01:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=34)
[2026-06-08T08:01:52] Searching for additional isoforms (remaining=35)
[2026-06-08T08:01:53] Assigning confidence scores to events 
[2026-06-08T08:01:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:01:54] Writing fusions to file 'PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:01:55] Writing discarded fusions to file 'PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:02:09] Freeing resources
[2026-06-08T08:02:23] Done (elapsed time=00:05:46, CPU time=00:05:44, peak memory=10.1gb)