[2026-06-04T21:20:44] Launching Arriba 2.4.0
[2026-06-04T21:20:44] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:20:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:20:58] Reading chimeric alignments from '659_epP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11570812)
[2026-06-04T21:27:42] Marking multi-mapping alignments (marked=7321168)
[2026-06-04T21:27:45] Detecting strandedness (reverse)
[2026-06-04T21:27:45] Assigning strands to alignments 
[2026-06-04T21:27:47] Annotating alignments 
[2026-06-04T21:28:15] Filtering duplicates (remaining=6669352)
[2026-06-04T21:28:21] 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=6312156)
[2026-06-04T21:28:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6312156)
[2026-06-04T21:28:25] Filtering viral contigs with expression lower than the top 5 (remaining=6312156)
[2026-06-04T21:28:29] Filtering viral contigs with less than 5% coverage (remaining=6312156)
[2026-06-04T21:28:31] Estimating fragment length (mate gap mean=-89.026, mate gap stddev=29.1443, read length mean=136.897)
[2026-06-04T21:28:31] Filtering read-through fragments with a distance <=10000bp (remaining=5776771)
[2026-06-04T21:28:33] Filtering inconsistently clipped mates (remaining=5673729)
[2026-06-04T21:28:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5442189)
[2026-06-04T21:28:39] Filtering fragments with small insert size (remaining=5441343)
[2026-06-04T21:28:40] Filtering alignments with long gaps (remaining=5441343)
[2026-06-04T21:28:42] Filtering fragments with both mates in the same gene (remaining=5440435)
[2026-06-04T21:28:44] Filtering fusions arising from hairpin structures (remaining=5056864)
[2026-06-04T21:28:47] Filtering reads with a mismatch p-value <=0.01 (remaining=2711901)
[2026-06-04T21:28:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=1218128)
[2026-06-04T21:29:07] Finding fusions and counting supporting reads (total=909144)
[2026-06-04T21:29:21] Merging adjacent fusion breakpoints (remaining=899756)
[2026-06-04T21:29:23] Filtering multi-mapping fusions by alignment score and read support (remaining=544399)
[2026-06-04T21:29:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:29:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=540802)
[2026-06-04T21:29:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=280436)
[2026-06-04T21:29:56] Filtering fusions with <2 supporting reads (remaining=40227)
[2026-06-04T21:29:56] Filtering fusions with an e-value >=0.3 (remaining=14858)
[2026-06-04T21:29:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14919)
[2026-06-04T21:30:00] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14743)
[2026-06-04T21:30:01] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14744)
[2026-06-04T21:30:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7537)
[2026-06-04T21:30:07] Searching for fusions with spliced split reads (remaining=7562)
[2026-06-04T21:30:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=4547)
[2026-06-04T21:30:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4502)
[2026-06-04T21:30:13] Searching for fusions with >=4 spliced events (remaining=5452)
[2026-06-04T21:30:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2090)
[2026-06-04T21:30:27] Filtering fusions with anchors <=23nt (remaining=1685)
[2026-06-04T21:30:28] Filtering end-to-end fusions with low support (remaining=1608)
[2026-06-04T21:30:28] Filtering fusions with no coverage around the breakpoints (remaining=1541)
[2026-06-04T21:30:29] Indexing gene sequences 
[2026-06-04T21:30:34] Filtering genes with >=30% identity (remaining=445)
[2026-06-04T21:30:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=165)
[2026-06-04T21:30:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=151)
[2026-06-04T21:30:40] Searching for additional isoforms (remaining=228)
[2026-06-04T21:30:41] Assigning confidence scores to events 
[2026-06-04T21:30:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:30:44] Writing fusions to file '659_epP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:30:45] Writing discarded fusions to file '659_epP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:31:08] Freeing resources
[2026-06-04T21:31:26] Done (elapsed time=00:10:42, CPU time=00:10:40, peak memory=16.5gb)