[2026-06-08T08:20:12] Launching Arriba 2.4.0
[2026-06-08T08:20:12] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:24] Reading chimeric alignments from '659_6i-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=9043322)
[2026-06-08T08:24:53] Marking multi-mapping alignments (marked=5721136)
[2026-06-08T08:24:57] Detecting strandedness (reverse)
[2026-06-08T08:24:57] Assigning strands to alignments 
[2026-06-08T08:24:59] Annotating alignments 
[2026-06-08T08:25:29] Filtering duplicates (remaining=3215048)
[2026-06-08T08:25:34] 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=3109510)
[2026-06-08T08:25:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3109510)
[2026-06-08T08:25:37] Filtering viral contigs with expression lower than the top 5 (remaining=3109510)
[2026-06-08T08:25:41] Filtering viral contigs with less than 5% coverage (remaining=3109510)
[2026-06-08T08:25:43] Estimating fragment length (mate gap mean=-90.1703, mate gap stddev=26.9017, read length mean=131.087)
[2026-06-08T08:25:43] Filtering read-through fragments with a distance <=10000bp (remaining=2947477)
[2026-06-08T08:25:45] Filtering inconsistently clipped mates (remaining=2899835)
[2026-06-08T08:25:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2757572)
[2026-06-08T08:25:49] Filtering fragments with small insert size (remaining=2757064)
[2026-06-08T08:25:51] Filtering alignments with long gaps (remaining=2757063)
[2026-06-08T08:25:53] Filtering fragments with both mates in the same gene (remaining=2756508)
[2026-06-08T08:25:55] Filtering fusions arising from hairpin structures (remaining=2634751)
[2026-06-08T08:25:57] Filtering reads with a mismatch p-value <=0.01 (remaining=1191982)
[2026-06-08T08:26:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=419197)
[2026-06-08T08:26:10] Finding fusions and counting supporting reads (total=368626)
[2026-06-08T08:26:23] Merging adjacent fusion breakpoints (remaining=366317)
[2026-06-08T08:26:24] Filtering multi-mapping fusions by alignment score and read support (remaining=195482)
[2026-06-08T08:26:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:26:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=194414)
[2026-06-08T08:26:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=115061)
[2026-06-08T08:26:59] Filtering fusions with <2 supporting reads (remaining=11929)
[2026-06-08T08:26:59] Filtering fusions with an e-value >=0.3 (remaining=3022)
[2026-06-08T08:27:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3053)
[2026-06-08T08:27:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2980)
[2026-06-08T08:27:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2982)
[2026-06-08T08:27:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2922)
[2026-06-08T08:27:07] Searching for fusions with spliced split reads (remaining=2959)
[2026-06-08T08:27:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=2232)
[2026-06-08T08:27:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2203)
[2026-06-08T08:27:13] Searching for fusions with >=4 spliced events (remaining=2436)
[2026-06-08T08:27:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=713)
[2026-06-08T08:27:26] Filtering fusions with anchors <=23nt (remaining=601)
[2026-06-08T08:27:27] Filtering end-to-end fusions with low support (remaining=580)
[2026-06-08T08:27:27] Filtering fusions with no coverage around the breakpoints (remaining=561)
[2026-06-08T08:27:27] Indexing gene sequences 
[2026-06-08T08:27:30] Filtering genes with >=30% identity (remaining=211)
[2026-06-08T08:27:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=110)
[2026-06-08T08:27:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=99)
[2026-06-08T08:27:34] Searching for additional isoforms (remaining=119)
[2026-06-08T08:27:35] Assigning confidence scores to events 
[2026-06-08T08:27:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:27:37] Writing fusions to file '659_6i-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T08:27:37] Writing discarded fusions to file '659_6i-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:27:55] Freeing resources
[2026-06-08T08:28:10] Done (elapsed time=00:07:58, CPU time=00:07:56, peak memory=13.3gb)