[2026-06-08T08:34:47] Launching Arriba 2.4.0
[2026-06-08T08:34:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:03] Reading chimeric alignments from '659_cRa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10549160)
[2026-06-08T08:41:54] Marking multi-mapping alignments (marked=6352736)
[2026-06-08T08:41:58] Detecting strandedness (reverse)
[2026-06-08T08:41:58] Assigning strands to alignments 
[2026-06-08T08:42:00] Annotating alignments 
[2026-06-08T08:42:30] Filtering duplicates (remaining=7085330)
[2026-06-08T08:42:37] 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)
[2026-06-08T08:42:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6774557)
[2026-06-08T08:42:41] Filtering viral contigs with expression lower than the top 5 (remaining=6774557)
[2026-06-08T08:42:45] Filtering viral contigs with less than 5% coverage (remaining=6774557)
[2026-06-08T08:42:47] Estimating fragment length (mate gap mean=-84.2812, mate gap stddev=29.673, read length mean=130.579)
[2026-06-08T08:42:47] Filtering read-through fragments with a distance <=10000bp (remaining=6406930)
[2026-06-08T08:42:49] Filtering inconsistently clipped mates (remaining=6289712)
[2026-06-08T08:42:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6056839)
[2026-06-08T08:42:55] Filtering fragments with small insert size (remaining=6055075)
[2026-06-08T08:42:57] Filtering alignments with long gaps (remaining=6055075)
[2026-06-08T08:42:59] Filtering fragments with both mates in the same gene (remaining=6053843)
[2026-06-08T08:43:01] Filtering fusions arising from hairpin structures (remaining=5673818)
[2026-06-08T08:43:03] Filtering reads with a mismatch p-value <=0.01 (remaining=3029836)
[2026-06-08T08:43:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=1212336)
[2026-06-08T08:43:30] Finding fusions and counting supporting reads (total=870080)
[2026-06-08T08:43:45] Merging adjacent fusion breakpoints (remaining=862660)
[2026-06-08T08:43:47] Filtering multi-mapping fusions by alignment score and read support (remaining=549555)
[2026-06-08T08:44:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=547368)
[2026-06-08T08:44:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=329630)
[2026-06-08T08:44:23] Filtering fusions with <2 supporting reads (remaining=42060)
[2026-06-08T08:44:24] Filtering fusions with an e-value >=0.3 (remaining=11537)
[2026-06-08T08:44:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11622)
[2026-06-08T08:44:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11525)
[2026-06-08T08:44:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11525)
[2026-06-08T08:44:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7525)
[2026-06-08T08:44:35] Searching for fusions with spliced split reads (remaining=7560)
[2026-06-08T08:44:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=4626)
[2026-06-08T08:44:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4568)
[2026-06-08T08:44:42] Searching for fusions with >=4 spliced events (remaining=5480)
[2026-06-08T08:44:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2085)
[2026-06-08T08:44:57] Filtering fusions with anchors <=23nt (remaining=1587)
[2026-06-08T08:44:58] Filtering end-to-end fusions with low support (remaining=1559)
[2026-06-08T08:44:59] Filtering fusions with no coverage around the breakpoints (remaining=1522)
[2026-06-08T08:45:00] Indexing gene sequences 
[2026-06-08T08:45:06] Filtering genes with >=30% identity (remaining=473)
[2026-06-08T08:45:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=222)
[2026-06-08T08:45:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=193)
[2026-06-08T08:45:14] Searching for additional isoforms (remaining=248)
[2026-06-08T08:45:15] Assigning confidence scores to events 
[2026-06-08T08:45:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:19] Writing fusions to file '659_cRa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:20] Writing discarded fusions to file '659_cRa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:48] Freeing resources
[2026-06-08T08:46:06] Done (elapsed time=00:11:19, CPU time=00:11:18, peak memory=15gb)