[2026-06-08T08:23:44] Launching Arriba 2.4.0
[2026-06-08T08:23:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:24:00] Reading chimeric alignments from '659_mK-T1-TRNA-2_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12206419)
[2026-06-08T08:30:15] Marking multi-mapping alignments (marked=8264493)
[2026-06-08T08:30:19] Detecting strandedness (no)
[2026-06-08T08:30:19] Annotating alignments 
[2026-06-08T08:30:55] Filtering duplicates (remaining=7198847)
[2026-06-08T08:31:02] 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=6714778)
[2026-06-08T08:31:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6714778)
[2026-06-08T08:31:07] Filtering viral contigs with expression lower than the top 5 (remaining=6714778)
[2026-06-08T08:31:11] Filtering viral contigs with less than 5% coverage (remaining=6714778)
[2026-06-08T08:31:13] Estimating fragment length (mate gap mean=-82.0751, mate gap stddev=27.6501, read length mean=119.762)
[2026-06-08T08:31:14] Filtering read-through fragments with a distance <=10000bp (remaining=6391073)
[2026-06-08T08:31:16] Filtering inconsistently clipped mates (remaining=6245090)
[2026-06-08T08:31:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6084006)
[2026-06-08T08:31:22] Filtering fragments with small insert size (remaining=6082621)
[2026-06-08T08:31:24] Filtering alignments with long gaps (remaining=6082620)
[2026-06-08T08:31:26] Filtering fragments with both mates in the same gene (remaining=6081492)
[2026-06-08T08:31:28] Filtering fusions arising from hairpin structures (remaining=5664083)
[2026-06-08T08:31:30] Filtering reads with a mismatch p-value <=0.01 (remaining=2629212)
[2026-06-08T08:31:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=961334)
[2026-06-08T08:31:54] Finding fusions and counting supporting reads (total=746502)
[2026-06-08T08:32:09] Merging adjacent fusion breakpoints (remaining=735942)
[2026-06-08T08:32:11] Filtering multi-mapping fusions by alignment score and read support (remaining=426084)
[2026-06-08T08:32:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=424857)
[2026-06-08T08:32:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=266296)
[2026-06-08T08:32:51] Filtering fusions with <2 supporting reads (remaining=25663)
[2026-06-08T08:32:52] Filtering fusions with an e-value >=0.3 (remaining=5530)
[2026-06-08T08:32:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5601)
[2026-06-08T08:32:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5452)
[2026-06-08T08:32:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5454)
[2026-06-08T08:32:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5364)
[2026-06-08T08:33:03] Searching for fusions with spliced split reads (remaining=5466)
[2026-06-08T08:33:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=3846)
[2026-06-08T08:33:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3803)
[2026-06-08T08:33:10] Searching for fusions with >=4 spliced events (remaining=4545)
[2026-06-08T08:33:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1986)
[2026-06-08T08:33:25] Filtering fusions with anchors <=23nt (remaining=1489)
[2026-06-08T08:33:25] Filtering end-to-end fusions with low support (remaining=1455)
[2026-06-08T08:33:26] Filtering fusions with no coverage around the breakpoints (remaining=1433)
[2026-06-08T08:33:27] Indexing gene sequences 
[2026-06-08T08:33:32] Filtering genes with >=30% identity (remaining=497)
[2026-06-08T08:33:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=203)
[2026-06-08T08:33:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=175)
[2026-06-08T08:33:39] Searching for additional isoforms (remaining=213)
[2026-06-08T08:33:40] Assigning confidence scores to events 
[2026-06-08T08:33:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:33:44] Writing fusions to file '659_mK-T1-TRNA-2_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:33:45] Writing discarded fusions to file '659_mK-T1-TRNA-2_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:13] Freeing resources
[2026-06-08T08:34:31] Done (elapsed time=00:10:47, CPU time=00:10:46, peak memory=16.7gb)