[2026-06-08T08:30:52] Launching Arriba 2.4.0
[2026-06-08T08:30:52] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:08] Reading chimeric alignments from '659_ePR-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10033614)
[2026-06-08T08:37:38] Marking multi-mapping alignments (marked=6292948)
[2026-06-08T08:37:41] Detecting strandedness (reverse)
[2026-06-08T08:37:41] Assigning strands to alignments 
[2026-06-08T08:37:43] Annotating alignments 
[2026-06-08T08:38:12] Filtering duplicates (remaining=6102136)
[2026-06-08T08:38:19] 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=5735319)
[2026-06-08T08:38:21] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5735319)
[2026-06-08T08:38:23] Filtering viral contigs with expression lower than the top 5 (remaining=5735319)
[2026-06-08T08:38:27] Filtering viral contigs with less than 5% coverage (remaining=5735319)
[2026-06-08T08:38:29] Estimating fragment length (mate gap mean=-88.5549, mate gap stddev=28.2054, read length mean=132.294)
[2026-06-08T08:38:29] Filtering read-through fragments with a distance <=10000bp (remaining=5423897)
[2026-06-08T08:38:31] Filtering inconsistently clipped mates (remaining=5324110)
[2026-06-08T08:38:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5143533)
[2026-06-08T08:38:36] Filtering fragments with small insert size (remaining=5142776)
[2026-06-08T08:38:38] Filtering alignments with long gaps (remaining=5142776)
[2026-06-08T08:38:40] Filtering fragments with both mates in the same gene (remaining=5141671)
[2026-06-08T08:38:42] Filtering fusions arising from hairpin structures (remaining=4824717)
[2026-06-08T08:38:44] Filtering reads with a mismatch p-value <=0.01 (remaining=2473407)
[2026-06-08T08:38:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=1092172)
[2026-06-08T08:39:06] Finding fusions and counting supporting reads (total=760493)
[2026-06-08T08:39:20] Merging adjacent fusion breakpoints (remaining=755236)
[2026-06-08T08:39:22] Filtering multi-mapping fusions by alignment score and read support (remaining=477650)
[2026-06-08T08:39:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=475285)
[2026-06-08T08:39:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=280808)
[2026-06-08T08:39:56] Filtering fusions with <2 supporting reads (remaining=36305)
[2026-06-08T08:39:56] Filtering fusions with an e-value >=0.3 (remaining=9036)
[2026-06-08T08:39:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9086)
[2026-06-08T08:40:00] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8996)
[2026-06-08T08:40:01] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9002)
[2026-06-08T08:40:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7401)
[2026-06-08T08:40:06] Searching for fusions with spliced split reads (remaining=7540)
[2026-06-08T08:40:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=4691)
[2026-06-08T08:40:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4643)
[2026-06-08T08:40:12] Searching for fusions with >=4 spliced events (remaining=5553)
[2026-06-08T08:40:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1786)
[2026-06-08T08:40:26] Filtering fusions with anchors <=23nt (remaining=1425)
[2026-06-08T08:40:27] Filtering end-to-end fusions with low support (remaining=1402)
[2026-06-08T08:40:27] Filtering fusions with no coverage around the breakpoints (remaining=1364)
[2026-06-08T08:40:28] Indexing gene sequences 
[2026-06-08T08:40:33] Filtering genes with >=30% identity (remaining=408)
[2026-06-08T08:40:36] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=185)
[2026-06-08T08:40:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=171)
[2026-06-08T08:40:44] Searching for additional isoforms (remaining=219)
[2026-06-08T08:40:45] Assigning confidence scores to events 
[2026-06-08T08:40:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:48] Writing fusions to file '659_ePR-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:40:50] Writing discarded fusions to file '659_ePR-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:14] Freeing resources
[2026-06-08T08:41:30] Done (elapsed time=00:10:38, CPU time=00:10:37, peak memory=14.7gb)