[2026-06-08T07:55:29] Launching Arriba 2.4.0
[2026-06-08T07:55:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:55:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:55:52] Reading chimeric alignments from '659_eu1-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=6189852)
[2026-06-08T08:00:10] Marking multi-mapping alignments (marked=4279508)
[2026-06-08T08:00:12] Detecting strandedness (reverse)
[2026-06-08T08:00:12] Assigning strands to alignments 
[2026-06-08T08:00:13] Annotating alignments 
[2026-06-08T08:00:36] Filtering duplicates (remaining=3932149)
[2026-06-08T08:00:42] 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=3670253)
[2026-06-08T08:00:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3670253)
[2026-06-08T08:00:45] Filtering viral contigs with expression lower than the top 5 (remaining=3670253)
[2026-06-08T08:00:48] Filtering viral contigs with less than 5% coverage (remaining=3670253)
[2026-06-08T08:00:49] Estimating fragment length (mate gap mean=-78.7743, mate gap stddev=27.6858, read length mean=113.836)
[2026-06-08T08:00:49] Filtering read-through fragments with a distance <=10000bp (remaining=3456384)
[2026-06-08T08:00:51] Filtering inconsistently clipped mates (remaining=3401389)
[2026-06-08T08:00:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3274590)
[2026-06-08T08:00:55] Filtering fragments with small insert size (remaining=3273553)
[2026-06-08T08:00:56] Filtering alignments with long gaps (remaining=3273553)
[2026-06-08T08:00:57] Filtering fragments with both mates in the same gene (remaining=3272620)
[2026-06-08T08:00:59] Filtering fusions arising from hairpin structures (remaining=3154132)
[2026-06-08T08:01:00] Filtering reads with a mismatch p-value <=0.01 (remaining=1369841)
[2026-06-08T08:01:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=515146)
[2026-06-08T08:01:15] Finding fusions and counting supporting reads (total=411427)
[2026-06-08T08:01:27] Merging adjacent fusion breakpoints (remaining=407777)
[2026-06-08T08:01:28] Filtering multi-mapping fusions by alignment score and read support (remaining=219935)
[2026-06-08T08:01:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:01:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=219303)
[2026-06-08T08:01:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=146734)
[2026-06-08T08:01:56] Filtering fusions with <2 supporting reads (remaining=15078)
[2026-06-08T08:01:56] Filtering fusions with an e-value >=0.3 (remaining=3493)
[2026-06-08T08:01:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3526)
[2026-06-08T08:01:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3483)
[2026-06-08T08:01:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3488)
[2026-06-08T08:02:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3478)
[2026-06-08T08:02:04] Searching for fusions with spliced split reads (remaining=3513)
[2026-06-08T08:02:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=2550)
[2026-06-08T08:02:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2520)
[2026-06-08T08:02:09] Searching for fusions with >=4 spliced events (remaining=2837)
[2026-06-08T08:02:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1213)
[2026-06-08T08:02:30] Filtering fusions with anchors <=23nt (remaining=988)
[2026-06-08T08:02:30] Filtering end-to-end fusions with low support (remaining=954)
[2026-06-08T08:02:31] Filtering fusions with no coverage around the breakpoints (remaining=925)
[2026-06-08T08:02:31] Indexing gene sequences 
[2026-06-08T08:02:36] Filtering genes with >=30% identity (remaining=340)
[2026-06-08T08:02:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=188)
[2026-06-08T08:02:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=168)
[2026-06-08T08:02:42] Searching for additional isoforms (remaining=209)
[2026-06-08T08:02:43] Assigning confidence scores to events 
[2026-06-08T08:02:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:02:46] Writing fusions to file '659_eu1-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:02:47] Writing discarded fusions to file '659_eu1-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:03:11] Freeing resources
[2026-06-08T08:03:23] Done (elapsed time=00:07:54, CPU time=00:07:54, peak memory=10.5gb)