[2026-06-08T08:36:49] Launching Arriba 2.4.0
[2026-06-08T08:36:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:04] Reading chimeric alignments from '659_bIB-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9526112)
[2026-06-08T08:43:54] Marking multi-mapping alignments (marked=5751275)
[2026-06-08T08:43:58] Detecting strandedness (reverse)
[2026-06-08T08:43:58] Assigning strands to alignments 
[2026-06-08T08:43:59] Annotating alignments 
[2026-06-08T08:44:27] Filtering duplicates (remaining=6941389)
[2026-06-08T08:44:34] 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=6626263)
[2026-06-08T08:44:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6626263)
[2026-06-08T08:44:37] Filtering viral contigs with expression lower than the top 5 (remaining=6626263)
[2026-06-08T08:44:41] Filtering viral contigs with less than 5% coverage (remaining=6626263)
[2026-06-08T08:44:43] Estimating fragment length (mate gap mean=-86.6957, mate gap stddev=29.9432, read length mean=135.346)
[2026-06-08T08:44:43] Filtering read-through fragments with a distance <=10000bp (remaining=6107743)
[2026-06-08T08:44:45] Filtering inconsistently clipped mates (remaining=6017301)
[2026-06-08T08:44:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5855835)
[2026-06-08T08:44:51] Filtering fragments with small insert size (remaining=5855059)
[2026-06-08T08:44:53] Filtering alignments with long gaps (remaining=5855058)
[2026-06-08T08:44:55] Filtering fragments with both mates in the same gene (remaining=5853977)
[2026-06-08T08:44:57] Filtering fusions arising from hairpin structures (remaining=5510429)
[2026-06-08T08:44:59] Filtering reads with a mismatch p-value <=0.01 (remaining=3074617)
[2026-06-08T08:45:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=1421174)
[2026-06-08T08:45:26] Finding fusions and counting supporting reads (total=982740)
[2026-06-08T08:45:40] Merging adjacent fusion breakpoints (remaining=972454)
[2026-06-08T08:45:42] Filtering multi-mapping fusions by alignment score and read support (remaining=636057)
[2026-06-08T08:46:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=633179)
[2026-06-08T08:46:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=341225)
[2026-06-08T08:46:17] Filtering fusions with <2 supporting reads (remaining=48563)
[2026-06-08T08:46:17] Filtering fusions with an e-value >=0.3 (remaining=14140)
[2026-06-08T08:46:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14198)
[2026-06-08T08:46:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14105)
[2026-06-08T08:46:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14108)
[2026-06-08T08:46:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9955)
[2026-06-08T08:46:28] Searching for fusions with spliced split reads (remaining=9983)
[2026-06-08T08:46:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=5344)
[2026-06-08T08:46:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5283)
[2026-06-08T08:46:34] Searching for fusions with >=4 spliced events (remaining=6603)
[2026-06-08T08:46:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2437)
[2026-06-08T08:46:51] Filtering fusions with anchors <=23nt (remaining=1955)
[2026-06-08T08:46:51] Filtering end-to-end fusions with low support (remaining=1920)
[2026-06-08T08:46:52] Filtering fusions with no coverage around the breakpoints (remaining=1878)
[2026-06-08T08:46:53] Indexing gene sequences 
[2026-06-08T08:47:00] Filtering genes with >=30% identity (remaining=671)
[2026-06-08T08:47:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=376)
[2026-06-08T08:47:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=236)
[2026-06-08T08:47:16] Searching for additional isoforms (remaining=353)
[2026-06-08T08:47:18] Assigning confidence scores to events 
[2026-06-08T08:47:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:21] Writing fusions to file '659_bIB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:24] Writing discarded fusions to file '659_bIB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:51] Freeing resources
[2026-06-08T08:48:07] Done (elapsed time=00:11:18, CPU time=00:11:17, peak memory=14.3gb)