[2026-06-08T08:10:32] Launching Arriba 2.4.0
[2026-06-08T08:10:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:10:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:10:45] Reading chimeric alignments from '659_Dl-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9117337)
[2026-06-08T08:15:24] Marking multi-mapping alignments (marked=6174120)
[2026-06-08T08:15:27] Detecting strandedness (reverse)
[2026-06-08T08:15:27] Assigning strands to alignments 
[2026-06-08T08:15:29] Annotating alignments 
[2026-06-08T08:15:59] Filtering duplicates (remaining=4901018)
[2026-06-08T08:16:05] 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=4603629)
[2026-06-08T08:16:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4603629)
[2026-06-08T08:16:08] Filtering viral contigs with expression lower than the top 5 (remaining=4603629)
[2026-06-08T08:16:12] Filtering viral contigs with less than 5% coverage (remaining=4603629)
[2026-06-08T08:16:14] Estimating fragment length (mate gap mean=-84.116, mate gap stddev=27.5774, read length mean=122.697)
[2026-06-08T08:16:14] Filtering read-through fragments with a distance <=10000bp (remaining=4408963)
[2026-06-08T08:16:16] Filtering inconsistently clipped mates (remaining=4299393)
[2026-06-08T08:16:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4137270)
[2026-06-08T08:16:21] Filtering fragments with small insert size (remaining=4136213)
[2026-06-08T08:16:23] Filtering alignments with long gaps (remaining=4136213)
[2026-06-08T08:16:25] Filtering fragments with both mates in the same gene (remaining=4135290)
[2026-06-08T08:16:26] Filtering fusions arising from hairpin structures (remaining=3819541)
[2026-06-08T08:16:29] Filtering reads with a mismatch p-value <=0.01 (remaining=1824296)
[2026-06-08T08:16:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=639872)
[2026-06-08T08:16:47] Finding fusions and counting supporting reads (total=487695)
[2026-06-08T08:17:02] Merging adjacent fusion breakpoints (remaining=482352)
[2026-06-08T08:17:03] Filtering multi-mapping fusions by alignment score and read support (remaining=267052)
[2026-06-08T08:17:33] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:17:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=265899)
[2026-06-08T08:17:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=157645)
[2026-06-08T08:17:40] Filtering fusions with <2 supporting reads (remaining=18617)
[2026-06-08T08:17:41] Filtering fusions with an e-value >=0.3 (remaining=4503)
[2026-06-08T08:17:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4574)
[2026-06-08T08:17:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4482)
[2026-06-08T08:17:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4483)
[2026-06-08T08:17:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4341)
[2026-06-08T08:17:50] Searching for fusions with spliced split reads (remaining=4415)
[2026-06-08T08:17:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=3159)
[2026-06-08T08:17:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3119)
[2026-06-08T08:17:56] Searching for fusions with >=4 spliced events (remaining=3543)
[2026-06-08T08:17:57] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1344)
[2026-06-08T08:18:10] Filtering fusions with anchors <=23nt (remaining=1015)
[2026-06-08T08:18:11] Filtering end-to-end fusions with low support (remaining=992)
[2026-06-08T08:18:11] Filtering fusions with no coverage around the breakpoints (remaining=975)
[2026-06-08T08:18:12] Indexing gene sequences 
[2026-06-08T08:18:16] Filtering genes with >=30% identity (remaining=351)
[2026-06-08T08:18:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=201)
[2026-06-08T08:18:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=173)
[2026-06-08T08:18:23] Searching for additional isoforms (remaining=213)
[2026-06-08T08:18:24] Assigning confidence scores to events 
[2026-06-08T08:18:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:18:27] Writing fusions to file '659_Dl-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:18:28] Writing discarded fusions to file '659_Dl-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:53] Freeing resources
[2026-06-08T08:19:08] Done (elapsed time=00:08:36, CPU time=00:08:35, peak memory=13.5gb)