[2026-06-08T08:30:51] Launching Arriba 2.4.0
[2026-06-08T08:30:51] 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_SP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9478342)
[2026-06-08T08:38:14] Marking multi-mapping alignments (marked=5879901)
[2026-06-08T08:38:18] Detecting strandedness (reverse)
[2026-06-08T08:38:18] Assigning strands to alignments 
[2026-06-08T08:38:20] Annotating alignments 
[2026-06-08T08:38:48] Filtering duplicates (remaining=6439095)
[2026-06-08T08:38:55] 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=6168037)
[2026-06-08T08:38:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6168037)
[2026-06-08T08:38:58] Filtering viral contigs with expression lower than the top 5 (remaining=6168037)
[2026-06-08T08:39:02] Filtering viral contigs with less than 5% coverage (remaining=6168037)
[2026-06-08T08:39:04] Estimating fragment length (mate gap mean=-87.6716, mate gap stddev=28.0988, read length mean=129.797)
[2026-06-08T08:39:04] Filtering read-through fragments with a distance <=10000bp (remaining=5793837)
[2026-06-08T08:39:05] Filtering inconsistently clipped mates (remaining=5681515)
[2026-06-08T08:39:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5500209)
[2026-06-08T08:39:11] Filtering fragments with small insert size (remaining=5499343)
[2026-06-08T08:39:13] Filtering alignments with long gaps (remaining=5499343)
[2026-06-08T08:39:15] Filtering fragments with both mates in the same gene (remaining=5498304)
[2026-06-08T08:39:17] Filtering fusions arising from hairpin structures (remaining=5142954)
[2026-06-08T08:39:19] Filtering reads with a mismatch p-value <=0.01 (remaining=2682511)
[2026-06-08T08:39:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=1167528)
[2026-06-08T08:39:44] Finding fusions and counting supporting reads (total=813244)
[2026-06-08T08:39:59] Merging adjacent fusion breakpoints (remaining=803718)
[2026-06-08T08:40:00] Filtering multi-mapping fusions by alignment score and read support (remaining=496898)
[2026-06-08T08:40:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=495066)
[2026-06-08T08:40:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=279134)
[2026-06-08T08:40:35] Filtering fusions with <2 supporting reads (remaining=37322)
[2026-06-08T08:40:36] Filtering fusions with an e-value >=0.3 (remaining=9162)
[2026-06-08T08:40:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9237)
[2026-06-08T08:40:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9132)
[2026-06-08T08:40:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9136)
[2026-06-08T08:40:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8487)
[2026-06-08T08:40:46] Searching for fusions with spliced split reads (remaining=8633)
[2026-06-08T08:40:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=5382)
[2026-06-08T08:40:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5313)
[2026-06-08T08:40:52] Searching for fusions with >=4 spliced events (remaining=6285)
[2026-06-08T08:40:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2282)
[2026-06-08T08:41:09] Filtering fusions with anchors <=23nt (remaining=1813)
[2026-06-08T08:41:10] Filtering end-to-end fusions with low support (remaining=1768)
[2026-06-08T08:41:10] Filtering fusions with no coverage around the breakpoints (remaining=1729)
[2026-06-08T08:41:11] Indexing gene sequences 
[2026-06-08T08:41:17] Filtering genes with >=30% identity (remaining=518)
[2026-06-08T08:41:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=204)
[2026-06-08T08:41:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-08T08:41:29] Searching for additional isoforms (remaining=239)
[2026-06-08T08:41:30] Assigning confidence scores to events 
[2026-06-08T08:41:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:33] Writing fusions to file '659_SP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:35] Writing discarded fusions to file '659_SP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:03] Freeing resources
[2026-06-08T08:42:19] Done (elapsed time=00:11:28, CPU time=00:11:26, peak memory=14.1gb)