[2026-06-04T21:12:01] Launching Arriba 2.4.0
[2026-06-04T21:12:01] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:12:09] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:12:12] Reading chimeric alignments from '659_dts-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=13063380)
[2026-06-04T21:18:59] Marking multi-mapping alignments (marked=8472447)
[2026-06-04T21:19:04] Detecting strandedness (reverse)
[2026-06-04T21:19:04] Assigning strands to alignments 
[2026-06-04T21:19:07] Annotating alignments 
[2026-06-04T21:19:46] Filtering duplicates (remaining=8697615)
[2026-06-04T21:19:55] 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=8238349)
[2026-06-04T21:19:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8238349)
[2026-06-04T21:20:00] Filtering viral contigs with expression lower than the top 5 (remaining=8238349)
[2026-06-04T21:20:06] Filtering viral contigs with less than 5% coverage (remaining=8238349)
[2026-06-04T21:20:09] Estimating fragment length (mate gap mean=-84.4488, mate gap stddev=27.893, read length mean=124.533)
[2026-06-04T21:20:09] Filtering read-through fragments with a distance <=10000bp (remaining=7728936)
[2026-06-04T21:20:12] Filtering inconsistently clipped mates (remaining=7594350)
[2026-06-04T21:20:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7427743)
[2026-06-04T21:20:20] Filtering fragments with small insert size (remaining=7426273)
[2026-06-04T21:20:22] Filtering alignments with long gaps (remaining=7426273)
[2026-06-04T21:20:25] Filtering fragments with both mates in the same gene (remaining=7424927)
[2026-06-04T21:20:28] Filtering fusions arising from hairpin structures (remaining=7010543)
[2026-06-04T21:20:31] Filtering reads with a mismatch p-value <=0.01 (remaining=3458933)
[2026-06-04T21:20:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=1416104)
[2026-06-04T21:21:02] Finding fusions and counting supporting reads (total=1089850)
[2026-06-04T21:21:22] Merging adjacent fusion breakpoints (remaining=1078013)
[2026-06-04T21:21:24] Filtering multi-mapping fusions by alignment score and read support (remaining=661800)
[2026-06-04T21:22:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:22:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=659369)
[2026-06-04T21:22:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=407194)
[2026-06-04T21:22:16] Filtering fusions with <2 supporting reads (remaining=39879)
[2026-06-04T21:22:17] Filtering fusions with an e-value >=0.3 (remaining=8294)
[2026-06-04T21:22:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8379)
[2026-06-04T21:22:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8295)
[2026-06-04T21:22:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8296)
[2026-06-04T21:22:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7740)
[2026-06-04T21:22:33] Searching for fusions with spliced split reads (remaining=7774)
[2026-06-04T21:22:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=5136)
[2026-06-04T21:22:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5077)
[2026-06-04T21:22:43] Searching for fusions with >=4 spliced events (remaining=6142)
[2026-06-04T21:22:45] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2505)
[2026-06-04T21:23:02] Filtering fusions with anchors <=23nt (remaining=1904)
[2026-06-04T21:23:03] Filtering end-to-end fusions with low support (remaining=1847)
[2026-06-04T21:23:04] Filtering fusions with no coverage around the breakpoints (remaining=1804)
[2026-06-04T21:23:05] Indexing gene sequences 
[2026-06-04T21:23:11] Filtering genes with >=30% identity (remaining=606)
[2026-06-04T21:23:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=261)
[2026-06-04T21:23:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=216)
[2026-06-04T21:23:21] Searching for additional isoforms (remaining=270)
[2026-06-04T21:23:23] Assigning confidence scores to events 
[2026-06-04T21:23:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:23:28] Writing fusions to file '659_dts-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:23:30] Writing discarded fusions to file '659_dts-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:24:10] Freeing resources
[2026-06-04T21:24:33] Done (elapsed time=00:12:32, CPU time=00:12:30, peak memory=17.8gb)