[2026-06-04T21:18:01] Launching Arriba 2.4.0
[2026-06-04T21:18:01] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:18:09] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:18:13] Reading chimeric alignments from '659_bUW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=13108986)
[2026-06-04T21:25:48] Marking multi-mapping alignments (marked=8763411)
[2026-06-04T21:25:53] Detecting strandedness (reverse)
[2026-06-04T21:25:53] Assigning strands to alignments 
[2026-06-04T21:25:56] Annotating alignments 
[2026-06-04T21:26:33] Filtering duplicates (remaining=9394234)
[2026-06-04T21:26:42] 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=8866382)
[2026-06-04T21:26:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8866382)
[2026-06-04T21:26:47] Filtering viral contigs with expression lower than the top 5 (remaining=8866382)
[2026-06-04T21:26:53] Filtering viral contigs with less than 5% coverage (remaining=8866382)
[2026-06-04T21:26:56] Estimating fragment length (mate gap mean=-84.6587, mate gap stddev=29.2725, read length mean=131.472)
[2026-06-04T21:26:56] Filtering read-through fragments with a distance <=10000bp (remaining=8060275)
[2026-06-04T21:26:59] Filtering inconsistently clipped mates (remaining=7946315)
[2026-06-04T21:27:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7775347)
[2026-06-04T21:27:07] Filtering fragments with small insert size (remaining=7774421)
[2026-06-04T21:27:09] Filtering alignments with long gaps (remaining=7774421)
[2026-06-04T21:27:12] Filtering fragments with both mates in the same gene (remaining=7773216)
[2026-06-04T21:27:15] Filtering fusions arising from hairpin structures (remaining=7256502)
[2026-06-04T21:27:18] Filtering reads with a mismatch p-value <=0.01 (remaining=3826708)
[2026-06-04T21:27:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=1799457)
[2026-06-04T21:27:50] Finding fusions and counting supporting reads (total=1267273)
[2026-06-04T21:28:11] Merging adjacent fusion breakpoints (remaining=1246273)
[2026-06-04T21:28:14] Filtering multi-mapping fusions by alignment score and read support (remaining=745806)
[2026-06-04T21:28:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:29:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=744049)
[2026-06-04T21:29:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=419996)
[2026-06-04T21:29:05] Filtering fusions with <2 supporting reads (remaining=43202)
[2026-06-04T21:29:06] Filtering fusions with an e-value >=0.3 (remaining=10592)
[2026-06-04T21:29:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10652)
[2026-06-04T21:29:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10559)
[2026-06-04T21:29:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10565)
[2026-06-04T21:29:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8623)
[2026-06-04T21:29:22] Searching for fusions with spliced split reads (remaining=8642)
[2026-06-04T21:29:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=4765)
[2026-06-04T21:29:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4736)
[2026-06-04T21:29:31] Searching for fusions with >=4 spliced events (remaining=5943)
[2026-06-04T21:29:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2517)
[2026-06-04T21:29:47] Filtering fusions with anchors <=23nt (remaining=1935)
[2026-06-04T21:29:48] Filtering end-to-end fusions with low support (remaining=1899)
[2026-06-04T21:29:49] Filtering fusions with no coverage around the breakpoints (remaining=1860)
[2026-06-04T21:29:50] Indexing gene sequences 
[2026-06-04T21:29:56] Filtering genes with >=30% identity (remaining=536)
[2026-06-04T21:30:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=212)
[2026-06-04T21:30:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=178)
[2026-06-04T21:30:05] Searching for additional isoforms (remaining=253)
[2026-06-04T21:30:07] Assigning confidence scores to events 
[2026-06-04T21:30:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:30:11] Writing fusions to file '659_bUW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:30:14] Writing discarded fusions to file '659_bUW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:30:50] Freeing resources
[2026-06-04T21:31:13] Done (elapsed time=00:13:12, CPU time=00:13:10, peak memory=18gb)