[2026-06-08T08:28:51] Launching Arriba 2.4.0
[2026-06-08T08:28:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:04] Reading chimeric alignments from '659_cTi-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11960780)
[2026-06-08T08:35:56] Marking multi-mapping alignments (marked=7315636)
[2026-06-08T08:36:00] Detecting strandedness (reverse)
[2026-06-08T08:36:00] Assigning strands to alignments 
[2026-06-08T08:36:03] Annotating alignments 
[2026-06-08T08:36:43] Filtering duplicates (remaining=8381391)
[2026-06-08T08:36:52] 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=7956443)
[2026-06-08T08:36:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7956443)
[2026-06-08T08:36:56] Filtering viral contigs with expression lower than the top 5 (remaining=7956443)
[2026-06-08T08:37:02] Filtering viral contigs with less than 5% coverage (remaining=7956443)
[2026-06-08T08:37:04] Estimating fragment length (mate gap mean=-84.5685, mate gap stddev=28.6905, read length mean=127.984)
[2026-06-08T08:37:05] Filtering read-through fragments with a distance <=10000bp (remaining=7400546)
[2026-06-08T08:37:07] Filtering inconsistently clipped mates (remaining=7271336)
[2026-06-08T08:37:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7118744)
[2026-06-08T08:37:14] Filtering fragments with small insert size (remaining=7116975)
[2026-06-08T08:37:17] Filtering alignments with long gaps (remaining=7116974)
[2026-06-08T08:37:19] Filtering fragments with both mates in the same gene (remaining=7115664)
[2026-06-08T08:37:22] Filtering fusions arising from hairpin structures (remaining=6697525)
[2026-06-08T08:37:25] Filtering reads with a mismatch p-value <=0.01 (remaining=3436644)
[2026-06-08T08:37:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=1449898)
[2026-06-08T08:37:57] Finding fusions and counting supporting reads (total=1085987)
[2026-06-08T08:38:19] Merging adjacent fusion breakpoints (remaining=1076893)
[2026-06-08T08:38:21] Filtering multi-mapping fusions by alignment score and read support (remaining=688749)
[2026-06-08T08:39:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=686882)
[2026-06-08T08:39:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=402510)
[2026-06-08T08:39:13] Filtering fusions with <2 supporting reads (remaining=46771)
[2026-06-08T08:39:14] Filtering fusions with an e-value >=0.3 (remaining=11053)
[2026-06-08T08:39:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11114)
[2026-06-08T08:39:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11031)
[2026-06-08T08:39:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11033)
[2026-06-08T08:39:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9220)
[2026-06-08T08:39:29] Searching for fusions with spliced split reads (remaining=9237)
[2026-06-08T08:39:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=5689)
[2026-06-08T08:39:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5601)
[2026-06-08T08:39:38] Searching for fusions with >=4 spliced events (remaining=7119)
[2026-06-08T08:39:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2949)
[2026-06-08T08:39:59] Filtering fusions with anchors <=23nt (remaining=2248)
[2026-06-08T08:40:00] Filtering end-to-end fusions with low support (remaining=2201)
[2026-06-08T08:40:01] Filtering fusions with no coverage around the breakpoints (remaining=2140)
[2026-06-08T08:40:02] Indexing gene sequences 
[2026-06-08T08:40:08] Filtering genes with >=30% identity (remaining=641)
[2026-06-08T08:40:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=248)
[2026-06-08T08:40:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=198)
[2026-06-08T08:40:23] Searching for additional isoforms (remaining=265)
[2026-06-08T08:40:24] Assigning confidence scores to events 
[2026-06-08T08:40:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:29] Writing fusions to file '659_cTi-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:40:32] Writing discarded fusions to file '659_cTi-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:10] Freeing resources
[2026-06-08T08:41:29] Done (elapsed time=00:12:38, CPU time=00:12:37, peak memory=16.8gb)