[2026-06-08T09:04:19] Launching Arriba 2.4.0
[2026-06-08T09:04:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:04:33] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:04:37] Reading chimeric alignments from '659_bNS-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10853236)
[2026-06-08T09:12:46] Marking multi-mapping alignments (marked=6909182)
[2026-06-08T09:12:51] Detecting strandedness (reverse)
[2026-06-08T09:12:51] Assigning strands to alignments 
[2026-06-08T09:12:54] Annotating alignments 
[2026-06-08T09:13:31] Filtering duplicates (remaining=3766515)
[2026-06-08T09:13:37] 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=3548042)
[2026-06-08T09:13:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3548042)
[2026-06-08T09:13:42] Filtering viral contigs with expression lower than the top 5 (remaining=3548042)
[2026-06-08T09:13:46] Filtering viral contigs with less than 5% coverage (remaining=3548042)
[2026-06-08T09:13:49] Estimating fragment length (mate gap mean=-88.1066, mate gap stddev=29.213, read length mean=134.155)
[2026-06-08T09:13:49] Filtering read-through fragments with a distance <=10000bp (remaining=3384667)
[2026-06-08T09:13:51] Filtering inconsistently clipped mates (remaining=3338562)
[2026-06-08T09:13:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3211737)
[2026-06-08T09:13:57] Filtering fragments with small insert size (remaining=3211267)
[2026-06-08T09:13:59] Filtering alignments with long gaps (remaining=3211267)
[2026-06-08T09:14:02] Filtering fragments with both mates in the same gene (remaining=3210625)
[2026-06-08T09:14:04] Filtering fusions arising from hairpin structures (remaining=3063929)
[2026-06-08T09:14:06] Filtering reads with a mismatch p-value <=0.01 (remaining=1210931)
[2026-06-08T09:14:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=456097)
[2026-06-08T09:14:23] Finding fusions and counting supporting reads (total=378412)
[2026-06-08T09:14:39] Merging adjacent fusion breakpoints (remaining=374774)
[2026-06-08T09:14:40] Filtering multi-mapping fusions by alignment score and read support (remaining=230699)
[2026-06-08T09:15:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:15:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=229302)
[2026-06-08T09:15:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=125966)
[2026-06-08T09:15:18] Filtering fusions with <2 supporting reads (remaining=15701)
[2026-06-08T09:15:19] Filtering fusions with an e-value >=0.3 (remaining=4595)
[2026-06-08T09:15:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4617)
[2026-06-08T09:15:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4546)
[2026-06-08T09:15:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4546)
[2026-06-08T09:15:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3381)
[2026-06-08T09:15:28] Searching for fusions with spliced split reads (remaining=3522)
[2026-06-08T09:15:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=2471)
[2026-06-08T09:15:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2449)
[2026-06-08T09:15:33] Searching for fusions with >=4 spliced events (remaining=2720)
[2026-06-08T09:15:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=862)
[2026-06-08T09:15:49] Filtering fusions with anchors <=23nt (remaining=653)
[2026-06-08T09:15:49] Filtering end-to-end fusions with low support (remaining=610)
[2026-06-08T09:15:50] Filtering fusions with no coverage around the breakpoints (remaining=590)
[2026-06-08T09:15:50] Indexing gene sequences 
[2026-06-08T09:15:54] Filtering genes with >=30% identity (remaining=218)
[2026-06-08T09:15:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=118)
[2026-06-08T09:15:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=118)
[2026-06-08T09:15:58] Searching for additional isoforms (remaining=131)
[2026-06-08T09:15:58] Assigning confidence scores to events 
[2026-06-08T09:16:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:16:01] Writing fusions to file '659_bNS-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:16:02] Writing discarded fusions to file '659_bNS-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:16:21] Freeing resources
[2026-06-08T09:16:38] Done (elapsed time=00:12:19, CPU time=00:12:18, peak memory=15.4gb)