[2026-05-27T23:59:39] Launching Arriba 2.4.0
[2026-05-27T23:59:39] Loading assembly from 'ref_genome.fa' 
[2026-05-27T23:59:54] Loading annotation from 'ref_annot.gtf' 
[2026-05-27T23:59:59] Reading chimeric alignments from '659_Dl-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=4105148)
[2026-05-28T00:03:14] Marking multi-mapping alignments (marked=2855436)
[2026-05-28T00:03:16] Detecting strandedness (no)
[2026-05-28T00:03:16] Annotating alignments 
[2026-05-28T00:03:34] Filtering duplicates (remaining=1188714)
[2026-05-28T00:03:36] 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=1036778)
[2026-05-28T00:03:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1036778)
[2026-05-28T00:03:38] Filtering viral contigs with expression lower than the top 5 (remaining=1036778)
[2026-05-28T00:03:39] Filtering viral contigs with less than 5% coverage (remaining=1036778)
[2026-05-28T00:03:41] Estimating fragment length (mate gap mean=-87.1629, mate gap stddev=28.2772, read length mean=126.63)
[2026-05-28T00:03:41] Filtering read-through fragments with a distance <=10000bp (remaining=994134)
[2026-05-28T00:03:42] Filtering inconsistently clipped mates (remaining=971542)
[2026-05-28T00:03:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=911105)
[2026-05-28T00:03:44] Filtering fragments with small insert size (remaining=910829)
[2026-05-28T00:03:45] Filtering alignments with long gaps (remaining=910829)
[2026-05-28T00:03:46] Filtering fragments with both mates in the same gene (remaining=910556)
[2026-05-28T00:03:47] Filtering fusions arising from hairpin structures (remaining=861495)
[2026-05-28T00:03:48] Filtering reads with a mismatch p-value <=0.01 (remaining=329569)
[2026-05-28T00:03:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=126631)
[2026-05-28T00:03:54] Finding fusions and counting supporting reads (total=116713)
[2026-05-28T00:04:01] Merging adjacent fusion breakpoints (remaining=115778)
[2026-05-28T00:04:01] Filtering multi-mapping fusions by alignment score and read support (remaining=55523)
[2026-05-28T00:04:16] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:04:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=54884)
[2026-05-28T00:04:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=34578)
[2026-05-28T00:04:18] Filtering fusions with <2 supporting reads (remaining=2779)
[2026-05-28T00:04:18] Filtering fusions with an e-value >=0.3 (remaining=834)
[2026-05-28T00:04:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=846)
[2026-05-28T00:04:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=809)
[2026-05-28T00:04:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=809)
[2026-05-28T00:04:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=785)
[2026-05-28T00:04:21] Searching for fusions with spliced split reads (remaining=893)
[2026-05-28T00:04:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=687)
[2026-05-28T00:04:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=681)
[2026-05-28T00:04:23] Searching for fusions with >=4 spliced events (remaining=729)
[2026-05-28T00:04:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=238)
[2026-05-28T00:04:44] Filtering fusions with anchors <=23nt (remaining=200)
[2026-05-28T00:04:44] Filtering end-to-end fusions with low support (remaining=197)
[2026-05-28T00:04:44] Filtering fusions with no coverage around the breakpoints (remaining=184)
[2026-05-28T00:04:44] Indexing gene sequences 
[2026-05-28T00:04:48] Filtering genes with >=30% identity (remaining=86)
[2026-05-28T00:04:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=61)
[2026-05-28T00:04:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=57)
[2026-05-28T00:04:49] Searching for additional isoforms (remaining=66)
[2026-05-28T00:04:49] Assigning confidence scores to events 
[2026-05-28T00:04:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:04:50] Writing fusions to file '659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:04:51] Writing discarded fusions to file '659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:05:00] Freeing resources
[2026-05-28T00:05:11] Done (elapsed time=00:05:32, CPU time=00:05:31, peak memory=8.35gb)