[2026-06-08T08:29:51] Launching Arriba 2.4.0
[2026-06-08T08:29:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:05] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:10] Reading chimeric alignments from '659_bKP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11860002)
[2026-06-08T08:38:28] Marking multi-mapping alignments (marked=7835323)
[2026-06-08T08:38:34] Detecting strandedness (reverse)
[2026-06-08T08:38:34] Assigning strands to alignments 
[2026-06-08T08:38:38] Annotating alignments 
[2026-06-08T08:39:30] Filtering duplicates (remaining=6275851)
[2026-06-08T08:39:38] 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=5919930)
[2026-06-08T08:39:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5919930)
[2026-06-08T08:39:42] Filtering viral contigs with expression lower than the top 5 (remaining=5919930)
[2026-06-08T08:39:48] Filtering viral contigs with less than 5% coverage (remaining=5919930)
[2026-06-08T08:39:51] Estimating fragment length (mate gap mean=-88.8743, mate gap stddev=28.0032, read length mean=127.739)
[2026-06-08T08:39:51] Filtering read-through fragments with a distance <=10000bp (remaining=5492646)
[2026-06-08T08:39:53] Filtering inconsistently clipped mates (remaining=5385712)
[2026-06-08T08:39:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5179348)
[2026-06-08T08:40:00] Filtering fragments with small insert size (remaining=5178346)
[2026-06-08T08:40:02] Filtering alignments with long gaps (remaining=5178346)
[2026-06-08T08:40:04] Filtering fragments with both mates in the same gene (remaining=5177497)
[2026-06-08T08:40:07] Filtering fusions arising from hairpin structures (remaining=4841182)
[2026-06-08T08:40:09] Filtering reads with a mismatch p-value <=0.01 (remaining=2259108)
[2026-06-08T08:40:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=985749)
[2026-06-08T08:40:36] Finding fusions and counting supporting reads (total=771534)
[2026-06-08T08:40:55] Merging adjacent fusion breakpoints (remaining=758972)
[2026-06-08T08:40:57] Filtering multi-mapping fusions by alignment score and read support (remaining=452839)
[2026-06-08T08:41:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=451437)
[2026-06-08T08:41:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=243272)
[2026-06-08T08:41:43] Filtering fusions with <2 supporting reads (remaining=29409)
[2026-06-08T08:41:44] Filtering fusions with an e-value >=0.3 (remaining=6736)
[2026-06-08T08:41:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6778)
[2026-06-08T08:41:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6639)
[2026-06-08T08:41:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6642)
[2026-06-08T08:41:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6461)
[2026-06-08T08:41:56] Searching for fusions with spliced split reads (remaining=6555)
[2026-06-08T08:42:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=4544)
[2026-06-08T08:42:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4494)
[2026-06-08T08:42:04] Searching for fusions with >=4 spliced events (remaining=5271)
[2026-06-08T08:42:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2194)
[2026-06-08T08:42:27] Filtering fusions with anchors <=23nt (remaining=1596)
[2026-06-08T08:42:27] Filtering end-to-end fusions with low support (remaining=1548)
[2026-06-08T08:42:28] Filtering fusions with no coverage around the breakpoints (remaining=1503)
[2026-06-08T08:42:29] Indexing gene sequences 
[2026-06-08T08:42:34] Filtering genes with >=30% identity (remaining=417)
[2026-06-08T08:42:36] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=83)
[2026-06-08T08:42:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=82)
[2026-06-08T08:42:40] Searching for additional isoforms (remaining=113)
[2026-06-08T08:42:41] Assigning confidence scores to events 
[2026-06-08T08:42:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:45] Writing fusions to file '659_bKP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:46] Writing discarded fusions to file '659_bKP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:16] Freeing resources
[2026-06-08T08:43:36] Done (elapsed time=00:13:45, CPU time=00:13:44, peak memory=16.6gb)