[2026-06-08T08:44:17] Launching Arriba 2.4.0
[2026-06-08T08:44:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:44:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:44:30] Reading chimeric alignments from 'PX_FFPE_pan_TRNA_nat_01_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=13553937)
[2026-06-08T08:50:42] Marking multi-mapping alignments (marked=8788219)
[2026-06-08T08:50:47] Detecting strandedness (reverse)
[2026-06-08T08:50:47] Assigning strands to alignments 
[2026-06-08T08:50:50] Annotating alignments 
[2026-06-08T08:51:31] Filtering duplicates (remaining=3672958)
[2026-06-08T08:51:38] 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=3349692)
[2026-06-08T08:51:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3349692)
[2026-06-08T08:51:43] Filtering viral contigs with expression lower than the top 5 (remaining=3349692)
[2026-06-08T08:51:49] Filtering viral contigs with less than 5% coverage (remaining=3349692)
[2026-06-08T08:51:52] Estimating fragment length (mate gap mean=-87.8699, mate gap stddev=28.2317, read length mean=124.859)
[2026-06-08T08:51:52] Filtering read-through fragments with a distance <=10000bp (remaining=3139562)
[2026-06-08T08:51:55] Filtering inconsistently clipped mates (remaining=3083152)
[2026-06-08T08:51:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2884302)
[2026-06-08T08:52:01] Filtering fragments with small insert size (remaining=2883182)
[2026-06-08T08:52:04] Filtering alignments with long gaps (remaining=2883182)
[2026-06-08T08:52:07] Filtering fragments with both mates in the same gene (remaining=2882549)
[2026-06-08T08:52:10] Filtering fusions arising from hairpin structures (remaining=2772980)
[2026-06-08T08:52:12] Filtering reads with a mismatch p-value <=0.01 (remaining=1133531)
[2026-06-08T08:52:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=477281)
[2026-06-08T08:52:30] Finding fusions and counting supporting reads (total=322392)
[2026-06-08T08:52:47] Merging adjacent fusion breakpoints (remaining=317236)
[2026-06-08T08:52:48] Filtering multi-mapping fusions by alignment score and read support (remaining=172673)
[2026-06-08T08:53:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=171888)
[2026-06-08T08:53:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=115167)
[2026-06-08T08:53:33] Filtering fusions with <2 supporting reads (remaining=24733)
[2026-06-08T08:53:33] Filtering fusions with an e-value >=0.3 (remaining=10180)
[2026-06-08T08:53:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10204)
[2026-06-08T08:53:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10163)
[2026-06-08T08:53:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10163)
[2026-06-08T08:53:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2683)
[2026-06-08T08:53:43] Searching for fusions with spliced split reads (remaining=2759)
[2026-06-08T08:53:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=1878)
[2026-06-08T08:53:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1871)
[2026-06-08T08:53:49] Searching for fusions with >=4 spliced events (remaining=2099)
[2026-06-08T08:53:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=537)
[2026-06-08T08:54:02] Filtering fusions with anchors <=23nt (remaining=430)
[2026-06-08T08:54:02] Filtering end-to-end fusions with low support (remaining=420)
[2026-06-08T08:54:03] Filtering fusions with no coverage around the breakpoints (remaining=403)
[2026-06-08T08:54:03] Indexing gene sequences 
[2026-06-08T08:54:05] Filtering genes with >=30% identity (remaining=121)
[2026-06-08T08:54:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=54)
[2026-06-08T08:54:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=51)
[2026-06-08T08:54:07] Searching for additional isoforms (remaining=63)
[2026-06-08T08:54:08] Assigning confidence scores to events 
[2026-06-08T08:54:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:09] Writing fusions to file 'PX_FFPE_pan_TRNA_nat_01_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:10] Writing discarded fusions to file 'PX_FFPE_pan_TRNA_nat_01_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:26] Freeing resources
[2026-06-08T08:54:46] Done (elapsed time=00:10:29, CPU time=00:10:28, peak memory=17.7gb)