[2026-06-08T08:34:39] Launching Arriba 2.4.0
[2026-06-08T08:34:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:52] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=13568738)
[2026-06-08T08:41:39] Marking multi-mapping alignments (marked=8652929)
[2026-06-08T08:41:44] Detecting strandedness (reverse)
[2026-06-08T08:41:44] Assigning strands to alignments 
[2026-06-08T08:41:47] Annotating alignments 
[2026-06-08T08:42:32] Filtering duplicates (remaining=3693927)
[2026-06-08T08:42:38] 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=3526683)
[2026-06-08T08:42:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3526683)
[2026-06-08T08:42:43] Filtering viral contigs with expression lower than the top 5 (remaining=3526683)
[2026-06-08T08:42:49] Filtering viral contigs with less than 5% coverage (remaining=3526683)
[2026-06-08T08:42:52] Estimating fragment length (mate gap mean=-88.3056, mate gap stddev=26.6001, read length mean=127.96)
[2026-06-08T08:42:52] Filtering read-through fragments with a distance <=10000bp (remaining=3344958)
[2026-06-08T08:42:55] Filtering inconsistently clipped mates (remaining=3291272)
[2026-06-08T08:42:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3157693)
[2026-06-08T08:43:01] Filtering fragments with small insert size (remaining=3157128)
[2026-06-08T08:43:04] Filtering alignments with long gaps (remaining=3157128)
[2026-06-08T08:43:07] Filtering fragments with both mates in the same gene (remaining=3156510)
[2026-06-08T08:43:10] Filtering fusions arising from hairpin structures (remaining=3035798)
[2026-06-08T08:43:13] Filtering reads with a mismatch p-value <=0.01 (remaining=1330645)
[2026-06-08T08:43:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=440505)
[2026-06-08T08:43:31] Finding fusions and counting supporting reads (total=381790)
[2026-06-08T08:43:49] Merging adjacent fusion breakpoints (remaining=378767)
[2026-06-08T08:43:50] Filtering multi-mapping fusions by alignment score and read support (remaining=207883)
[2026-06-08T08:44:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=206992)
[2026-06-08T08:44:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=123210)
[2026-06-08T08:44:40] Filtering fusions with <2 supporting reads (remaining=12872)
[2026-06-08T08:44:41] Filtering fusions with an e-value >=0.3 (remaining=3220)
[2026-06-08T08:44:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3239)
[2026-06-08T08:44:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3177)
[2026-06-08T08:44:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3177)
[2026-06-08T08:44:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3067)
[2026-06-08T08:44:51] Searching for fusions with spliced split reads (remaining=3108)
[2026-06-08T08:44:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=2228)
[2026-06-08T08:44:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2203)
[2026-06-08T08:44:57] Searching for fusions with >=4 spliced events (remaining=2439)
[2026-06-08T08:44:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=774)
[2026-06-08T08:45:10] Filtering fusions with anchors <=23nt (remaining=685)
[2026-06-08T08:45:11] Filtering end-to-end fusions with low support (remaining=662)
[2026-06-08T08:45:11] Filtering fusions with no coverage around the breakpoints (remaining=637)
[2026-06-08T08:45:12] Indexing gene sequences 
[2026-06-08T08:45:15] Filtering genes with >=30% identity (remaining=232)
[2026-06-08T08:45:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=95)
[2026-06-08T08:45:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=88)
[2026-06-08T08:45:18] Searching for additional isoforms (remaining=109)
[2026-06-08T08:45:19] Assigning confidence scores to events 
[2026-06-08T08:45:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:21] Writing fusions to file 'BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:45:22] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:42] Freeing resources
[2026-06-08T08:46:03] Done (elapsed time=00:11:24, CPU time=00:11:23, peak memory=17.7gb)