[2026-06-08T08:58:32] Launching Arriba 2.4.0
[2026-06-08T08:58:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:58:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:46] Reading chimeric alignments from '659_bTo-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=10636974)
[2026-06-08T09:05:57] Marking multi-mapping alignments (marked=6125019)
[2026-06-08T09:06:01] Detecting strandedness (reverse)
[2026-06-08T09:06:01] Assigning strands to alignments 
[2026-06-08T09:06:03] Annotating alignments 
[2026-06-08T09:06:40] Filtering duplicates (remaining=7120026)
[2026-06-08T09:06:49] 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=6975301)
[2026-06-08T09:06:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6975301)
[2026-06-08T09:06:53] Filtering viral contigs with expression lower than the top 5 (remaining=6975301)
[2026-06-08T09:06:58] Filtering viral contigs with less than 5% coverage (remaining=6975301)
[2026-06-08T09:07:00] Estimating fragment length (mate gap mean=-88.2443, mate gap stddev=30.4582, read length mean=139.898)
[2026-06-08T09:07:00] Filtering read-through fragments with a distance <=10000bp (remaining=6535829)
[2026-06-08T09:07:03] Filtering inconsistently clipped mates (remaining=6445450)
[2026-06-08T09:07:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6285022)
[2026-06-08T09:07:09] Filtering fragments with small insert size (remaining=6284346)
[2026-06-08T09:07:11] Filtering alignments with long gaps (remaining=6284346)
[2026-06-08T09:07:14] Filtering fragments with both mates in the same gene (remaining=6283367)
[2026-06-08T09:07:16] Filtering fusions arising from hairpin structures (remaining=5909180)
[2026-06-08T09:07:19] Filtering reads with a mismatch p-value <=0.01 (remaining=3123365)
[2026-06-08T09:07:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=1137060)
[2026-06-08T09:07:48] Finding fusions and counting supporting reads (total=851040)
[2026-06-08T09:08:07] Merging adjacent fusion breakpoints (remaining=842687)
[2026-06-08T09:08:09] Filtering multi-mapping fusions by alignment score and read support (remaining=599817)
[2026-06-08T09:08:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:08:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=597820)
[2026-06-08T09:08:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=298094)
[2026-06-08T09:08:56] Filtering fusions with <2 supporting reads (remaining=49064)
[2026-06-08T09:08:57] Filtering fusions with an e-value >=0.3 (remaining=17489)
[2026-06-08T09:08:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17541)
[2026-06-08T09:09:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=17461)
[2026-06-08T09:09:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17461)
[2026-06-08T09:09:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8994)
[2026-06-08T09:09:10] Searching for fusions with spliced split reads (remaining=9015)
[2026-06-08T09:09:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=4961)
[2026-06-08T09:09:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4921)
[2026-06-08T09:09:18] Searching for fusions with >=4 spliced events (remaining=6269)
[2026-06-08T09:09:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2427)
[2026-06-08T09:09:33] Filtering fusions with anchors <=23nt (remaining=2005)
[2026-06-08T09:09:33] Filtering end-to-end fusions with low support (remaining=1960)
[2026-06-08T09:09:34] Filtering fusions with no coverage around the breakpoints (remaining=1925)
[2026-06-08T09:09:35] Indexing gene sequences 
[2026-06-08T09:09:42] Filtering genes with >=30% identity (remaining=560)
[2026-06-08T09:09:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=240)
[2026-06-08T09:09:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=206)
[2026-06-08T09:09:54] Searching for additional isoforms (remaining=269)
[2026-06-08T09:09:55] Assigning confidence scores to events 
[2026-06-08T09:09:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:59] Writing fusions to file '659_bTo-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:10:01] Writing discarded fusions to file '659_bTo-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:33] Freeing resources
[2026-06-08T09:10:53] Done (elapsed time=00:12:21, CPU time=00:12:21, peak memory=15.1gb)