[2026-06-04T21:19:44] Launching Arriba 2.4.0
[2026-06-04T21:19:44] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:19:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:19:55] Reading chimeric alignments from '659_eZ4-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10453888)
[2026-06-04T21:26:24] Marking multi-mapping alignments (marked=6548118)
[2026-06-04T21:26:29] Detecting strandedness (reverse)
[2026-06-04T21:26:29] Assigning strands to alignments 
[2026-06-04T21:26:31] Annotating alignments 
[2026-06-04T21:27:03] Filtering duplicates (remaining=7517192)
[2026-06-04T21:27:11] 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=7089780)
[2026-06-04T21:27:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7089780)
[2026-06-04T21:27:15] Filtering viral contigs with expression lower than the top 5 (remaining=7089780)
[2026-06-04T21:27:20] Filtering viral contigs with less than 5% coverage (remaining=7089780)
[2026-06-04T21:27:23] Estimating fragment length (mate gap mean=-84.7247, mate gap stddev=31.0808, read length mean=134.263)
[2026-06-04T21:27:23] Filtering read-through fragments with a distance <=10000bp (remaining=6727727)
[2026-06-04T21:27:25] Filtering inconsistently clipped mates (remaining=6620170)
[2026-06-04T21:27:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6364151)
[2026-06-04T21:27:32] Filtering fragments with small insert size (remaining=6363136)
[2026-06-04T21:27:34] Filtering alignments with long gaps (remaining=6363136)
[2026-06-04T21:27:36] Filtering fragments with both mates in the same gene (remaining=6361801)
[2026-06-04T21:27:39] Filtering fusions arising from hairpin structures (remaining=5944658)
[2026-06-04T21:27:41] Filtering reads with a mismatch p-value <=0.01 (remaining=3222339)
[2026-06-04T21:27:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=1225181)
[2026-06-04T21:28:08] Finding fusions and counting supporting reads (total=906479)
[2026-06-04T21:28:25] Merging adjacent fusion breakpoints (remaining=901497)
[2026-06-04T21:28:27] Filtering multi-mapping fusions by alignment score and read support (remaining=562677)
[2026-06-04T21:28:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:29:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=559872)
[2026-06-04T21:29:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=365940)
[2026-06-04T21:29:08] Filtering fusions with <2 supporting reads (remaining=47099)
[2026-06-04T21:29:09] Filtering fusions with an e-value >=0.3 (remaining=18279)
[2026-06-04T21:29:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=18327)
[2026-06-04T21:29:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=18270)
[2026-06-04T21:29:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=18280)
[2026-06-04T21:29:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8575)
[2026-06-04T21:29:22] Searching for fusions with spliced split reads (remaining=8653)
[2026-06-04T21:29:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=4600)
[2026-06-04T21:29:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4554)
[2026-06-04T21:29:29] Searching for fusions with >=4 spliced events (remaining=5684)
[2026-06-04T21:29:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2157)
[2026-06-04T21:29:44] Filtering fusions with anchors <=23nt (remaining=1691)
[2026-06-04T21:29:44] Filtering end-to-end fusions with low support (remaining=1654)
[2026-06-04T21:29:45] Filtering fusions with no coverage around the breakpoints (remaining=1620)
[2026-06-04T21:29:46] Indexing gene sequences 
[2026-06-04T21:29:51] Filtering genes with >=30% identity (remaining=456)
[2026-06-04T21:29:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=216)
[2026-06-04T21:29:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=180)
[2026-06-04T21:30:00] Searching for additional isoforms (remaining=251)
[2026-06-04T21:30:02] Assigning confidence scores to events 
[2026-06-04T21:30:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:30:06] Writing fusions to file '659_eZ4-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:30:08] Writing discarded fusions to file '659_eZ4-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:30:38] Freeing resources
[2026-06-04T21:30:57] Done (elapsed time=00:11:13, CPU time=00:11:11, peak memory=15.1gb)