[2026-06-04T21:13:51] Launching Arriba 2.4.0
[2026-06-04T21:13:51] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:13:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:14:02] Reading chimeric alignments from '659_ciJ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12466511)
[2026-06-04T21:20:51] Marking multi-mapping alignments (marked=7774388)
[2026-06-04T21:20:56] Detecting strandedness (no)
[2026-06-04T21:20:56] Annotating alignments 
[2026-06-04T21:21:39] Filtering duplicates (remaining=8813217)
[2026-06-04T21:21:48] 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=8341132)
[2026-06-04T21:21:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8341132)
[2026-06-04T21:21:53] Filtering viral contigs with expression lower than the top 5 (remaining=8341132)
[2026-06-04T21:21:59] Filtering viral contigs with less than 5% coverage (remaining=8341132)
[2026-06-04T21:22:02] Estimating fragment length (mate gap mean=-85.0947, mate gap stddev=30.2146, read length mean=130.994)
[2026-06-04T21:22:02] Filtering read-through fragments with a distance <=10000bp (remaining=7837236)
[2026-06-04T21:22:05] Filtering inconsistently clipped mates (remaining=7696661)
[2026-06-04T21:22:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7426731)
[2026-06-04T21:22:12] Filtering fragments with small insert size (remaining=7425431)
[2026-06-04T21:22:15] Filtering alignments with long gaps (remaining=7425431)
[2026-06-04T21:22:17] Filtering fragments with both mates in the same gene (remaining=7424029)
[2026-06-04T21:22:20] Filtering fusions arising from hairpin structures (remaining=6859508)
[2026-06-04T21:22:23] Filtering reads with a mismatch p-value <=0.01 (remaining=3639637)
[2026-06-04T21:22:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=1473651)
[2026-06-04T21:22:52] Finding fusions and counting supporting reads (total=1157099)
[2026-06-04T21:23:10] Merging adjacent fusion breakpoints (remaining=1144030)
[2026-06-04T21:23:13] Filtering multi-mapping fusions by alignment score and read support (remaining=712021)
[2026-06-04T21:23:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:23:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=709142)
[2026-06-04T21:23:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=419267)
[2026-06-04T21:24:00] Filtering fusions with <2 supporting reads (remaining=47415)
[2026-06-04T21:24:01] Filtering fusions with an e-value >=0.3 (remaining=13988)
[2026-06-04T21:24:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14071)
[2026-06-04T21:24:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13932)
[2026-06-04T21:24:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13936)
[2026-06-04T21:24:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10276)
[2026-06-04T21:24:17] Searching for fusions with spliced split reads (remaining=10301)
[2026-06-04T21:24:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=5471)
[2026-06-04T21:24:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5412)
[2026-06-04T21:24:26] Searching for fusions with >=4 spliced events (remaining=6749)
[2026-06-04T21:24:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2620)
[2026-06-04T21:24:47] Filtering fusions with anchors <=23nt (remaining=1959)
[2026-06-04T21:24:48] Filtering end-to-end fusions with low support (remaining=1902)
[2026-06-04T21:24:49] Filtering fusions with no coverage around the breakpoints (remaining=1858)
[2026-06-04T21:24:50] Indexing gene sequences 
[2026-06-04T21:24:57] Filtering genes with >=30% identity (remaining=552)
[2026-06-04T21:25:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=242)
[2026-06-04T21:25:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=207)
[2026-06-04T21:25:11] Searching for additional isoforms (remaining=273)
[2026-06-04T21:25:13] Assigning confidence scores to events 
[2026-06-04T21:25:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:25:17] Writing fusions to file '659_ciJ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:25:20] Writing discarded fusions to file '659_ciJ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:25:52] Freeing resources
[2026-06-04T21:26:12] Done (elapsed time=00:12:21, CPU time=00:12:21, peak memory=17.4gb)