[2026-06-04T21:16:43] Launching Arriba 2.4.0
[2026-06-04T21:16:43] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:16:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:16:54] Reading chimeric alignments from '659_cRa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10549160)
[2026-06-04T21:23:30] Marking multi-mapping alignments (marked=6352736)
[2026-06-04T21:23:34] Detecting strandedness (reverse)
[2026-06-04T21:23:34] Assigning strands to alignments 
[2026-06-04T21:23:36] Annotating alignments 
[2026-06-04T21:24:05] Filtering duplicates (remaining=7085330)
[2026-06-04T21:24:12] 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=6774557)
[2026-06-04T21:24:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6774557)
[2026-06-04T21:24:16] Filtering viral contigs with expression lower than the top 5 (remaining=6774557)
[2026-06-04T21:24:21] Filtering viral contigs with less than 5% coverage (remaining=6774557)
[2026-06-04T21:24:23] Estimating fragment length (mate gap mean=-84.2812, mate gap stddev=29.673, read length mean=130.579)
[2026-06-04T21:24:23] Filtering read-through fragments with a distance <=10000bp (remaining=6406930)
[2026-06-04T21:24:25] Filtering inconsistently clipped mates (remaining=6289712)
[2026-06-04T21:24:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6056839)
[2026-06-04T21:24:31] Filtering fragments with small insert size (remaining=6055075)
[2026-06-04T21:24:33] Filtering alignments with long gaps (remaining=6055075)
[2026-06-04T21:24:35] Filtering fragments with both mates in the same gene (remaining=6053843)
[2026-06-04T21:24:38] Filtering fusions arising from hairpin structures (remaining=5673818)
[2026-06-04T21:24:40] Filtering reads with a mismatch p-value <=0.01 (remaining=3029836)
[2026-06-04T21:24:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=1212336)
[2026-06-04T21:25:04] Finding fusions and counting supporting reads (total=870080)
[2026-06-04T21:25:19] Merging adjacent fusion breakpoints (remaining=862660)
[2026-06-04T21:25:20] Filtering multi-mapping fusions by alignment score and read support (remaining=549555)
[2026-06-04T21:25:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:25:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=547368)
[2026-06-04T21:25:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=329630)
[2026-06-04T21:25:59] Filtering fusions with <2 supporting reads (remaining=42060)
[2026-06-04T21:25:59] Filtering fusions with an e-value >=0.3 (remaining=11537)
[2026-06-04T21:26:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11622)
[2026-06-04T21:26:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11525)
[2026-06-04T21:26:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11525)
[2026-06-04T21:26:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7525)
[2026-06-04T21:26:11] Searching for fusions with spliced split reads (remaining=7560)
[2026-06-04T21:26:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=4626)
[2026-06-04T21:26:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4568)
[2026-06-04T21:26:18] Searching for fusions with >=4 spliced events (remaining=5480)
[2026-06-04T21:26:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2085)
[2026-06-04T21:26:34] Filtering fusions with anchors <=23nt (remaining=1587)
[2026-06-04T21:26:34] Filtering end-to-end fusions with low support (remaining=1559)
[2026-06-04T21:26:35] Filtering fusions with no coverage around the breakpoints (remaining=1522)
[2026-06-04T21:26:36] Indexing gene sequences 
[2026-06-04T21:26:41] Filtering genes with >=30% identity (remaining=473)
[2026-06-04T21:26:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=222)
[2026-06-04T21:26:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=193)
[2026-06-04T21:26:49] Searching for additional isoforms (remaining=248)
[2026-06-04T21:26:50] Assigning confidence scores to events 
[2026-06-04T21:26:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:26:54] Writing fusions to file '659_cRa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:26:56] Writing discarded fusions to file '659_cRa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:27:21] Freeing resources
[2026-06-04T21:27:39] Done (elapsed time=00:10:56, CPU time=00:10:55, peak memory=15.1gb)