[2026-06-04T21:13:51] Launching Arriba 2.4.0
[2026-06-04T21:13:51] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:13:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:14:03] Reading chimeric alignments from '659_bTq-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10239092)
[2026-06-04T21:20:56] Marking multi-mapping alignments (marked=6479388)
[2026-06-04T21:21:01] Detecting strandedness (reverse)
[2026-06-04T21:21:01] Assigning strands to alignments 
[2026-06-04T21:21:03] Annotating alignments 
[2026-06-04T21:21:39] Filtering duplicates (remaining=7328459)
[2026-06-04T21:21:47] 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)
[2026-06-04T21:21:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6978954)
[2026-06-04T21:21:51] Filtering viral contigs with expression lower than the top 5 (remaining=6978954)
[2026-06-04T21:21:56] Filtering viral contigs with less than 5% coverage (remaining=6978954)
[2026-06-04T21:21:58] Estimating fragment length (mate gap mean=-84.016, mate gap stddev=31.0601, read length mean=133.862)
[2026-06-04T21:21:58] Filtering read-through fragments with a distance <=10000bp (remaining=6613112)
[2026-06-04T21:22:00] Filtering inconsistently clipped mates (remaining=6546739)
[2026-06-04T21:22:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6252124)
[2026-06-04T21:22:08] Filtering fragments with small insert size (remaining=6251549)
[2026-06-04T21:22:10] Filtering alignments with long gaps (remaining=6251549)
[2026-06-04T21:22:12] Filtering fragments with both mates in the same gene (remaining=6250507)
[2026-06-04T21:22:15] Filtering fusions arising from hairpin structures (remaining=6029838)
[2026-06-04T21:22:18] Filtering reads with a mismatch p-value <=0.01 (remaining=3263475)
[2026-06-04T21:22:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=1209650)
[2026-06-04T21:22:46] Finding fusions and counting supporting reads (total=872904)
[2026-06-04T21:23:04] Merging adjacent fusion breakpoints (remaining=868528)
[2026-06-04T21:23:06] Filtering multi-mapping fusions by alignment score and read support (remaining=549123)
[2026-06-04T21:23:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:23:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=546517)
[2026-06-04T21:23:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=350111)
[2026-06-04T21:23:53] Filtering fusions with <2 supporting reads (remaining=39710)
[2026-06-04T21:23:53] Filtering fusions with an e-value >=0.3 (remaining=13259)
[2026-06-04T21:23:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13313)
[2026-06-04T21:23:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13261)
[2026-06-04T21:23:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13263)
[2026-06-04T21:24:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9018)
[2026-06-04T21:24:06] Searching for fusions with spliced split reads (remaining=9073)
[2026-06-04T21:24:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=4478)
[2026-06-04T21:24:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4427)
[2026-06-04T21:24:14] Searching for fusions with >=4 spliced events (remaining=5504)
[2026-06-04T21:24:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2270)
[2026-06-04T21:24:30] Filtering fusions with anchors <=23nt (remaining=1682)
[2026-06-04T21:24:31] Filtering end-to-end fusions with low support (remaining=1642)
[2026-06-04T21:24:32] Filtering fusions with no coverage around the breakpoints (remaining=1610)
[2026-06-04T21:24:32] Indexing gene sequences 
[2026-06-04T21:24:39] Filtering genes with >=30% identity (remaining=535)
[2026-06-04T21:24:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=325)
[2026-06-04T21:24:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=252)
[2026-06-04T21:24:57] Searching for additional isoforms (remaining=322)
[2026-06-04T21:24:59] Assigning confidence scores to events 
[2026-06-04T21:25:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:25:03] Writing fusions to file '659_bTq-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:25:07] Writing discarded fusions to file '659_bTq-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:25:43] Freeing resources
[2026-06-04T21:26:01] Done (elapsed time=00:12:10, CPU time=00:12:09, peak memory=14.7gb)