[2026-06-04T21:04:44] Launching Arriba 2.4.0
[2026-06-04T21:04:44] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:04:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:04:58] Reading chimeric alignments from '659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11038013)
[2026-06-04T21:10:59] Marking multi-mapping alignments (marked=7140709)
[2026-06-04T21:11:03] Detecting strandedness (reverse)
[2026-06-04T21:11:03] Assigning strands to alignments 
[2026-06-04T21:11:04] Annotating alignments 
[2026-06-04T21:11:31] Filtering duplicates (remaining=6859688)
[2026-06-04T21:11:37] 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=6412110)
[2026-06-04T21:11:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6412110)
[2026-06-04T21:11:40] Filtering viral contigs with expression lower than the top 5 (remaining=6412110)
[2026-06-04T21:11:44] Filtering viral contigs with less than 5% coverage (remaining=6412110)
[2026-06-04T21:11:46] Estimating fragment length (mate gap mean=-83.8408, mate gap stddev=28.7548, read length mean=122.706)
[2026-06-04T21:11:46] Filtering read-through fragments with a distance <=10000bp (remaining=6150136)
[2026-06-04T21:11:48] Filtering inconsistently clipped mates (remaining=6065271)
[2026-06-04T21:11:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5841599)
[2026-06-04T21:11:53] Filtering fragments with small insert size (remaining=5840364)
[2026-06-04T21:11:55] Filtering alignments with long gaps (remaining=5840363)
[2026-06-04T21:11:57] Filtering fragments with both mates in the same gene (remaining=5839153)
[2026-06-04T21:11:59] Filtering fusions arising from hairpin structures (remaining=5579663)
[2026-06-04T21:12:01] Filtering reads with a mismatch p-value <=0.01 (remaining=2650948)
[2026-06-04T21:12:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=942944)
[2026-06-04T21:12:20] Finding fusions and counting supporting reads (total=718381)
[2026-06-04T21:12:32] Merging adjacent fusion breakpoints (remaining=713065)
[2026-06-04T21:12:34] Filtering multi-mapping fusions by alignment score and read support (remaining=441851)
[2026-06-04T21:12:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:13:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=440564)
[2026-06-04T21:13:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=277976)
[2026-06-04T21:13:06] Filtering fusions with <2 supporting reads (remaining=28028)
[2026-06-04T21:13:07] Filtering fusions with an e-value >=0.3 (remaining=5962)
[2026-06-04T21:13:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6025)
[2026-06-04T21:13:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5964)
[2026-06-04T21:13:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5965)
[2026-06-04T21:13:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5803)
[2026-06-04T21:13:17] Searching for fusions with spliced split reads (remaining=5913)
[2026-06-04T21:13:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=4135)
[2026-06-04T21:13:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4094)
[2026-06-04T21:13:24] Searching for fusions with >=4 spliced events (remaining=4737)
[2026-06-04T21:13:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1585)
[2026-06-04T21:13:39] Filtering fusions with anchors <=23nt (remaining=1083)
[2026-06-04T21:13:40] Filtering end-to-end fusions with low support (remaining=1052)
[2026-06-04T21:13:40] Filtering fusions with no coverage around the breakpoints (remaining=1022)
[2026-06-04T21:13:41] Indexing gene sequences 
[2026-06-04T21:13:45] Filtering genes with >=30% identity (remaining=353)
[2026-06-04T21:13:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=170)
[2026-06-04T21:13:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-04T21:13:52] Searching for additional isoforms (remaining=207)
[2026-06-04T21:13:53] Assigning confidence scores to events 
[2026-06-04T21:13:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:13:56] Writing fusions to file '659_bGc-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:13:58] Writing discarded fusions to file '659_bGc-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:14:24] Freeing resources
[2026-06-04T21:14:39] Done (elapsed time=00:09:55, CPU time=00:09:55, peak memory=15.5gb)