[2026-06-08T08:06:30] Launching Arriba 2.4.0
[2026-06-08T08:06:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:06:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:06:51] Reading chimeric alignments from '659_cRB-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=6594273)
[2026-06-08T08:12:42] Marking multi-mapping alignments (marked=4233766)
[2026-06-08T08:12:45] Detecting strandedness (reverse)
[2026-06-08T08:12:45] Assigning strands to alignments 
[2026-06-08T08:12:46] Annotating alignments 
[2026-06-08T08:13:11] Filtering duplicates (remaining=3309401)
[2026-06-08T08:13:15] 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=3097514)
[2026-06-08T08:13:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3097514)
[2026-06-08T08:13:18] Filtering viral contigs with expression lower than the top 5 (remaining=3097514)
[2026-06-08T08:13:21] Filtering viral contigs with less than 5% coverage (remaining=3097514)
[2026-06-08T08:13:22] Estimating fragment length (mate gap mean=-86.7884, mate gap stddev=26.7366, read length mean=123.978)
[2026-06-08T08:13:22] Filtering read-through fragments with a distance <=10000bp (remaining=2898886)
[2026-06-08T08:13:24] Filtering inconsistently clipped mates (remaining=2845646)
[2026-06-08T08:13:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2754351)
[2026-06-08T08:13:28] Filtering fragments with small insert size (remaining=2753709)
[2026-06-08T08:13:29] Filtering alignments with long gaps (remaining=2753709)
[2026-06-08T08:13:31] Filtering fragments with both mates in the same gene (remaining=2753220)
[2026-06-08T08:13:32] Filtering fusions arising from hairpin structures (remaining=2607364)
[2026-06-08T08:13:34] Filtering reads with a mismatch p-value <=0.01 (remaining=1166484)
[2026-06-08T08:13:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=493218)
[2026-06-08T08:13:47] Finding fusions and counting supporting reads (total=384714)
[2026-06-08T08:13:58] Merging adjacent fusion breakpoints (remaining=380946)
[2026-06-08T08:13:59] Filtering multi-mapping fusions by alignment score and read support (remaining=227861)
[2026-06-08T08:14:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:14:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=227148)
[2026-06-08T08:14:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=131996)
[2026-06-08T08:14:25] Filtering fusions with <2 supporting reads (remaining=15801)
[2026-06-08T08:14:26] Filtering fusions with an e-value >=0.3 (remaining=3611)
[2026-06-08T08:14:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3647)
[2026-06-08T08:14:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3600)
[2026-06-08T08:14:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3600)
[2026-06-08T08:14:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3558)
[2026-06-08T08:14:32] Searching for fusions with spliced split reads (remaining=3589)
[2026-06-08T08:14:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=2623)
[2026-06-08T08:14:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2603)
[2026-06-08T08:14:37] Searching for fusions with >=4 spliced events (remaining=2892)
[2026-06-08T08:14:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=940)
[2026-06-08T08:14:55] Filtering fusions with anchors <=23nt (remaining=783)
[2026-06-08T08:14:55] Filtering end-to-end fusions with low support (remaining=761)
[2026-06-08T08:14:55] Filtering fusions with no coverage around the breakpoints (remaining=741)
[2026-06-08T08:14:56] Indexing gene sequences 
[2026-06-08T08:15:00] Filtering genes with >=30% identity (remaining=255)
[2026-06-08T08:15:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=106)
[2026-06-08T08:15:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=106)
[2026-06-08T08:15:05] Searching for additional isoforms (remaining=120)
[2026-06-08T08:15:05] Assigning confidence scores to events 
[2026-06-08T08:15:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:15:08] Writing fusions to file '659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:15:09] Writing discarded fusions to file '659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:15:30] Freeing resources
[2026-06-08T08:15:43] Done (elapsed time=00:09:13, CPU time=00:09:12, peak memory=11gb)