[2026-06-08T08:31:51] Launching Arriba 2.4.0
[2026-06-08T08:31:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:05] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:10] Reading chimeric alignments from '659_bTq-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10239092)
[2026-06-08T08:40:59] Marking multi-mapping alignments (marked=6479388)
[2026-06-08T08:41:04] Detecting strandedness (reverse)
[2026-06-08T08:41:04] Assigning strands to alignments 
[2026-06-08T08:41:06] Annotating alignments 
[2026-06-08T08:41:50] Filtering duplicates (remaining=7328459)
[2026-06-08T08:41:59] 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=6978954)
[2026-06-08T08:42:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6978954)
[2026-06-08T08:42:04] Filtering viral contigs with expression lower than the top 5 (remaining=6978954)
[2026-06-08T08:42:10] Filtering viral contigs with less than 5% coverage (remaining=6978954)
[2026-06-08T08:42:13] Estimating fragment length (mate gap mean=-84.016, mate gap stddev=31.0601, read length mean=133.862)
[2026-06-08T08:42:13] Filtering read-through fragments with a distance <=10000bp (remaining=6613112)
[2026-06-08T08:42:16] Filtering inconsistently clipped mates (remaining=6546739)
[2026-06-08T08:42:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6252124)
[2026-06-08T08:42:24] Filtering fragments with small insert size (remaining=6251549)
[2026-06-08T08:42:26] Filtering alignments with long gaps (remaining=6251549)
[2026-06-08T08:42:29] Filtering fragments with both mates in the same gene (remaining=6250507)
[2026-06-08T08:42:32] Filtering fusions arising from hairpin structures (remaining=6029838)
[2026-06-08T08:42:35] Filtering reads with a mismatch p-value <=0.01 (remaining=3263475)
[2026-06-08T08:42:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=1209650)
[2026-06-08T08:43:08] Finding fusions and counting supporting reads (total=872904)
[2026-06-08T08:43:35] Merging adjacent fusion breakpoints (remaining=868528)
[2026-06-08T08:43:37] Filtering multi-mapping fusions by alignment score and read support (remaining=549123)
[2026-06-08T08:44:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=546517)
[2026-06-08T08:44:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=350111)
[2026-06-08T08:44:34] Filtering fusions with <2 supporting reads (remaining=39710)
[2026-06-08T08:44:35] Filtering fusions with an e-value >=0.3 (remaining=13259)
[2026-06-08T08:44:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13313)
[2026-06-08T08:44:41] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13261)
[2026-06-08T08:44:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13263)
[2026-06-08T08:44:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9018)
[2026-06-08T08:44:51] Searching for fusions with spliced split reads (remaining=9073)
[2026-06-08T08:44:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=4478)
[2026-06-08T08:45:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4427)
[2026-06-08T08:45:01] Searching for fusions with >=4 spliced events (remaining=5504)
[2026-06-08T08:45:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2270)
[2026-06-08T08:45:25] Filtering fusions with anchors <=23nt (remaining=1682)
[2026-06-08T08:45:26] Filtering end-to-end fusions with low support (remaining=1642)
[2026-06-08T08:45:27] Filtering fusions with no coverage around the breakpoints (remaining=1610)
[2026-06-08T08:45:28] Indexing gene sequences 
[2026-06-08T08:45:38] Filtering genes with >=30% identity (remaining=535)
[2026-06-08T08:45:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=325)
[2026-06-08T08:46:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=252)
[2026-06-08T08:46:02] Searching for additional isoforms (remaining=322)
[2026-06-08T08:46:04] Assigning confidence scores to events 
[2026-06-08T08:46:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:09] Writing fusions to file '659_bTq-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:46:13] Writing discarded fusions to file '659_bTq-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:02] Freeing resources
[2026-06-08T08:47:26] Done (elapsed time=00:15:35, CPU time=00:15:35, peak memory=14.8gb)