[2026-06-08T08:30:49] Launching Arriba 2.4.0
[2026-06-08T08:30:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:03] Reading chimeric alignments from '659_dts-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=13063380)
[2026-06-08T08:38:57] Marking multi-mapping alignments (marked=8472447)
[2026-06-08T08:39:05] Detecting strandedness (reverse)
[2026-06-08T08:39:05] Assigning strands to alignments 
[2026-06-08T08:39:09] Annotating alignments 
[2026-06-08T08:40:16] Filtering duplicates (remaining=8697615)
[2026-06-08T08:40:29] 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)
[2026-06-08T08:40:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8238349)
[2026-06-08T08:40:37] Filtering viral contigs with expression lower than the top 5 (remaining=8238349)
[2026-06-08T08:40:46] Filtering viral contigs with less than 5% coverage (remaining=8238349)
[2026-06-08T08:40:50] Estimating fragment length (mate gap mean=-84.4488, mate gap stddev=27.893, read length mean=124.533)
[2026-06-08T08:40:50] Filtering read-through fragments with a distance <=10000bp (remaining=7728936)
[2026-06-08T08:40:54] Filtering inconsistently clipped mates (remaining=7594350)
[2026-06-08T08:40:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7427743)
[2026-06-08T08:41:06] Filtering fragments with small insert size (remaining=7426273)
[2026-06-08T08:41:10] Filtering alignments with long gaps (remaining=7426273)
[2026-06-08T08:41:14] Filtering fragments with both mates in the same gene (remaining=7424927)
[2026-06-08T08:41:18] Filtering fusions arising from hairpin structures (remaining=7010543)
[2026-06-08T08:41:22] Filtering reads with a mismatch p-value <=0.01 (remaining=3458933)
[2026-06-08T08:41:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=1416104)
[2026-06-08T08:42:03] Finding fusions and counting supporting reads (total=1089850)
[2026-06-08T08:42:40] Merging adjacent fusion breakpoints (remaining=1078013)
[2026-06-08T08:42:44] Filtering multi-mapping fusions by alignment score and read support (remaining=661800)
[2026-06-08T08:43:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=659369)
[2026-06-08T08:44:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=407194)
[2026-06-08T08:44:08] Filtering fusions with <2 supporting reads (remaining=39879)
[2026-06-08T08:44:10] Filtering fusions with an e-value >=0.3 (remaining=8294)
[2026-06-08T08:44:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8379)
[2026-06-08T08:44:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8295)
[2026-06-08T08:44:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8296)
[2026-06-08T08:44:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7740)
[2026-06-08T08:44:37] Searching for fusions with spliced split reads (remaining=7774)
[2026-06-08T08:44:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=5136)
[2026-06-08T08:44:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5077)
[2026-06-08T08:44:53] Searching for fusions with >=4 spliced events (remaining=6142)
[2026-06-08T08:44:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2505)
[2026-06-08T08:45:20] Filtering fusions with anchors <=23nt (remaining=1904)
[2026-06-08T08:45:22] Filtering end-to-end fusions with low support (remaining=1847)
[2026-06-08T08:45:24] Filtering fusions with no coverage around the breakpoints (remaining=1804)
[2026-06-08T08:45:26] Indexing gene sequences 
[2026-06-08T08:45:36] Filtering genes with >=30% identity (remaining=606)
[2026-06-08T08:45:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=261)
[2026-06-08T08:45:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=216)
[2026-06-08T08:45:53] Searching for additional isoforms (remaining=270)
[2026-06-08T08:45:56] Assigning confidence scores to events 
[2026-06-08T08:46:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:07] Writing fusions to file '659_dts-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:46:11] Writing discarded fusions to file '659_dts-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:28] Freeing resources
[2026-06-08T08:48:13] Done (elapsed time=00:17:24, CPU time=00:17:22, peak memory=17.8gb)