[2026-06-04T21:18:44] Launching Arriba 2.4.0
[2026-06-04T21:18:44] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:18:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:18:56] Reading chimeric alignments from '659_bIB-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9526112)
[2026-06-04T21:25:50] Marking multi-mapping alignments (marked=5751275)
[2026-06-04T21:25:53] Detecting strandedness (reverse)
[2026-06-04T21:25:53] Assigning strands to alignments 
[2026-06-04T21:25:55] Annotating alignments 
[2026-06-04T21:26:25] Filtering duplicates (remaining=6941389)
[2026-06-04T21:26:31] 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)
[2026-06-04T21:26:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6626263)
[2026-06-04T21:26:35] Filtering viral contigs with expression lower than the top 5 (remaining=6626263)
[2026-06-04T21:26:40] Filtering viral contigs with less than 5% coverage (remaining=6626263)
[2026-06-04T21:26:43] Estimating fragment length (mate gap mean=-86.6957, mate gap stddev=29.9432, read length mean=135.346)
[2026-06-04T21:26:43] Filtering read-through fragments with a distance <=10000bp (remaining=6107743)
[2026-06-04T21:26:45] Filtering inconsistently clipped mates (remaining=6017301)
[2026-06-04T21:26:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5855835)
[2026-06-04T21:26:51] Filtering fragments with small insert size (remaining=5855059)
[2026-06-04T21:26:53] Filtering alignments with long gaps (remaining=5855058)
[2026-06-04T21:26:55] Filtering fragments with both mates in the same gene (remaining=5853977)
[2026-06-04T21:26:57] Filtering fusions arising from hairpin structures (remaining=5510429)
[2026-06-04T21:27:00] Filtering reads with a mismatch p-value <=0.01 (remaining=3074617)
[2026-06-04T21:27:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=1421174)
[2026-06-04T21:27:26] Finding fusions and counting supporting reads (total=982740)
[2026-06-04T21:27:41] Merging adjacent fusion breakpoints (remaining=972454)
[2026-06-04T21:27:43] Filtering multi-mapping fusions by alignment score and read support (remaining=636057)
[2026-06-04T21:28:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:28:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=633179)
[2026-06-04T21:28:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=341225)
[2026-06-04T21:28:20] Filtering fusions with <2 supporting reads (remaining=48563)
[2026-06-04T21:28:21] Filtering fusions with an e-value >=0.3 (remaining=14140)
[2026-06-04T21:28:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14198)
[2026-06-04T21:28:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14105)
[2026-06-04T21:28:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14108)
[2026-06-04T21:28:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9955)
[2026-06-04T21:28:33] Searching for fusions with spliced split reads (remaining=9983)
[2026-06-04T21:28:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=5344)
[2026-06-04T21:28:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5283)
[2026-06-04T21:28:39] Searching for fusions with >=4 spliced events (remaining=6603)
[2026-06-04T21:28:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2437)
[2026-06-04T21:28:55] Filtering fusions with anchors <=23nt (remaining=1955)
[2026-06-04T21:28:55] Filtering end-to-end fusions with low support (remaining=1920)
[2026-06-04T21:28:56] Filtering fusions with no coverage around the breakpoints (remaining=1878)
[2026-06-04T21:28:57] Indexing gene sequences 
[2026-06-04T21:29:03] Filtering genes with >=30% identity (remaining=671)
[2026-06-04T21:29:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=376)
[2026-06-04T21:29:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=236)
[2026-06-04T21:29:18] Searching for additional isoforms (remaining=353)
[2026-06-04T21:29:19] Assigning confidence scores to events 
[2026-06-04T21:29:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:29:23] Writing fusions to file '659_bIB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:29:26] Writing discarded fusions to file '659_bIB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:29:53] Freeing resources
[2026-06-04T21:30:10] Done (elapsed time=00:11:26, CPU time=00:11:25, peak memory=14.3gb)