[2026-06-08T08:53:31] Launching Arriba 2.4.0
[2026-06-08T08:53:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:45] Reading chimeric alignments from 'PX_FFPE_gb_TRNA_nat_02_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=14703700)
[2026-06-08T09:01:32] Marking multi-mapping alignments (marked=9913756)
[2026-06-08T09:01:39] Detecting strandedness (reverse)
[2026-06-08T09:01:39] Assigning strands to alignments 
[2026-06-08T09:01:44] Annotating alignments 
[2026-06-08T09:02:35] Filtering duplicates (remaining=5809880)
[2026-06-08T09:02:44] 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=5485826)
[2026-06-08T09:02:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5485826)
[2026-06-08T09:02:50] Filtering viral contigs with expression lower than the top 5 (remaining=5485826)
[2026-06-08T09:02:57] Filtering viral contigs with less than 5% coverage (remaining=5485826)
[2026-06-08T09:03:00] Estimating fragment length (mate gap mean=-87.9165, mate gap stddev=28.1855, read length mean=131.262)
[2026-06-08T09:03:01] Filtering read-through fragments with a distance <=10000bp (remaining=5147005)
[2026-06-08T09:03:04] Filtering inconsistently clipped mates (remaining=5045039)
[2026-06-08T09:03:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4921128)
[2026-06-08T09:03:12] Filtering fragments with small insert size (remaining=4920172)
[2026-06-08T09:03:15] Filtering alignments with long gaps (remaining=4920172)
[2026-06-08T09:03:18] Filtering fragments with both mates in the same gene (remaining=4919382)
[2026-06-08T09:03:22] Filtering fusions arising from hairpin structures (remaining=4602630)
[2026-06-08T09:03:25] Filtering reads with a mismatch p-value <=0.01 (remaining=2178088)
[2026-06-08T09:03:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=690041)
[2026-06-08T09:03:50] Finding fusions and counting supporting reads (total=536608)
[2026-06-08T09:04:11] Merging adjacent fusion breakpoints (remaining=531332)
[2026-06-08T09:04:13] Filtering multi-mapping fusions by alignment score and read support (remaining=311056)
[2026-06-08T09:05:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:05:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=309029)
[2026-06-08T09:05:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=167670)
[2026-06-08T09:05:09] Filtering fusions with <2 supporting reads (remaining=19525)
[2026-06-08T09:05:10] Filtering fusions with an e-value >=0.3 (remaining=5850)
[2026-06-08T09:05:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5910)
[2026-06-08T09:05:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5856)
[2026-06-08T09:05:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5856)
[2026-06-08T09:05:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4570)
[2026-06-08T09:05:23] Searching for fusions with spliced split reads (remaining=4663)
[2026-06-08T09:05:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=3134)
[2026-06-08T09:05:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3094)
[2026-06-08T09:05:31] Searching for fusions with >=4 spliced events (remaining=3496)
[2026-06-08T09:05:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1160)
[2026-06-08T09:05:45] Filtering fusions with anchors <=23nt (remaining=990)
[2026-06-08T09:05:46] Filtering end-to-end fusions with low support (remaining=959)
[2026-06-08T09:05:46] Filtering fusions with no coverage around the breakpoints (remaining=936)
[2026-06-08T09:05:47] Indexing gene sequences 
[2026-06-08T09:05:51] Filtering genes with >=30% identity (remaining=305)
[2026-06-08T09:05:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=160)
[2026-06-08T09:05:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=154)
[2026-06-08T09:05:58] Searching for additional isoforms (remaining=179)
[2026-06-08T09:05:59] Assigning confidence scores to events 
[2026-06-08T09:06:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:06:02] Writing fusions to file 'PX_FFPE_gb_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:06:04] Writing discarded fusions to file 'PX_FFPE_gb_TRNA_nat_02_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:30] Freeing resources
[2026-06-08T09:06:54] Done (elapsed time=00:13:23, CPU time=00:13:21, peak memory=19gb)