[2026-06-08T08:57:47] Launching Arriba 2.4.0
[2026-06-08T08:57:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:57:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:01] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_07_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=12591495)
[2026-06-08T09:05:15] Marking multi-mapping alignments (marked=8114098)
[2026-06-08T09:05:20] Detecting strandedness (no)
[2026-06-08T09:05:20] Annotating alignments 
[2026-06-08T09:06:08] Filtering duplicates (remaining=7912712)
[2026-06-08T09:06:16] 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=7570878)
[2026-06-08T09:06:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7570878)
[2026-06-08T09:06:21] Filtering viral contigs with expression lower than the top 5 (remaining=7570878)
[2026-06-08T09:06:27] Filtering viral contigs with less than 5% coverage (remaining=7570878)
[2026-06-08T09:06:30] Estimating fragment length (mate gap mean=-87.7848, mate gap stddev=28.2865, read length mean=131.347)
[2026-06-08T09:06:30] Filtering read-through fragments with a distance <=10000bp (remaining=7032697)
[2026-06-08T09:06:32] Filtering inconsistently clipped mates (remaining=6881268)
[2026-06-08T09:06:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6737801)
[2026-06-08T09:06:41] Filtering fragments with small insert size (remaining=6736601)
[2026-06-08T09:06:43] Filtering alignments with long gaps (remaining=6736600)
[2026-06-08T09:06:46] Filtering fragments with both mates in the same gene (remaining=6735559)
[2026-06-08T09:06:49] Filtering fusions arising from hairpin structures (remaining=6253623)
[2026-06-08T09:06:52] Filtering reads with a mismatch p-value <=0.01 (remaining=3169849)
[2026-06-08T09:07:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=1349606)
[2026-06-08T09:07:23] Finding fusions and counting supporting reads (total=1017644)
[2026-06-08T09:07:42] Merging adjacent fusion breakpoints (remaining=1002478)
[2026-06-08T09:07:44] Filtering multi-mapping fusions by alignment score and read support (remaining=594032)
[2026-06-08T09:08:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:08:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=591594)
[2026-06-08T09:08:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=346509)
[2026-06-08T09:08:35] Filtering fusions with <2 supporting reads (remaining=39235)
[2026-06-08T09:08:36] Filtering fusions with an e-value >=0.3 (remaining=9135)
[2026-06-08T09:08:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9212)
[2026-06-08T09:08:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9073)
[2026-06-08T09:08:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9074)
[2026-06-08T09:08:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7993)
[2026-06-08T09:08:51] Searching for fusions with spliced split reads (remaining=8019)
[2026-06-08T09:08:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=5038)
[2026-06-08T09:08:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4988)
[2026-06-08T09:08:59] Searching for fusions with >=4 spliced events (remaining=6245)
[2026-06-08T09:09:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2646)
[2026-06-08T09:09:17] Filtering fusions with anchors <=23nt (remaining=2102)
[2026-06-08T09:09:18] Filtering end-to-end fusions with low support (remaining=2064)
[2026-06-08T09:09:19] Filtering fusions with no coverage around the breakpoints (remaining=2023)
[2026-06-08T09:09:20] Indexing gene sequences 
[2026-06-08T09:09:26] Filtering genes with >=30% identity (remaining=579)
[2026-06-08T09:09:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=227)
[2026-06-08T09:09:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=213)
[2026-06-08T09:09:37] Searching for additional isoforms (remaining=283)
[2026-06-08T09:09:39] Assigning confidence scores to events 
[2026-06-08T09:09:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:43] Writing fusions to file 'BVT_FFPE_TRNA_stm_07_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:09:45] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_07_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:18] Freeing resources
[2026-06-08T09:10:40] Done (elapsed time=00:12:53, CPU time=00:12:52, peak memory=17.3gb)