[2026-06-08T08:53:18] Launching Arriba 2.4.0
[2026-06-08T08:53:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:27] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:32] Reading chimeric alignments from '659_ezg-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10791759)
[2026-06-08T09:00:34] Marking multi-mapping alignments (marked=6920607)
[2026-06-08T09:00:39] Detecting strandedness (reverse)
[2026-06-08T09:00:39] Assigning strands to alignments 
[2026-06-08T09:00:42] Annotating alignments 
[2026-06-08T09:01:20] Filtering duplicates (remaining=4002920)
[2026-06-08T09:01:26] 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=3774970)
[2026-06-08T09:01:29] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3774970)
[2026-06-08T09:01:31] Filtering viral contigs with expression lower than the top 5 (remaining=3774970)
[2026-06-08T09:01:35] Filtering viral contigs with less than 5% coverage (remaining=3774970)
[2026-06-08T09:01:38] Estimating fragment length (mate gap mean=-88.7638, mate gap stddev=27.8524, read length mean=132.27)
[2026-06-08T09:01:38] Filtering read-through fragments with a distance <=10000bp (remaining=3533353)
[2026-06-08T09:01:40] Filtering inconsistently clipped mates (remaining=3480336)
[2026-06-08T09:01:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3349876)
[2026-06-08T09:01:46] Filtering fragments with small insert size (remaining=3349431)
[2026-06-08T09:01:49] Filtering alignments with long gaps (remaining=3349431)
[2026-06-08T09:01:51] Filtering fragments with both mates in the same gene (remaining=3348817)
[2026-06-08T09:01:54] Filtering fusions arising from hairpin structures (remaining=3193215)
[2026-06-08T09:01:56] Filtering reads with a mismatch p-value <=0.01 (remaining=1362520)
[2026-06-08T09:02:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=581172)
[2026-06-08T09:02:14] Finding fusions and counting supporting reads (total=485144)
[2026-06-08T09:02:31] Merging adjacent fusion breakpoints (remaining=479087)
[2026-06-08T09:02:32] Filtering multi-mapping fusions by alignment score and read support (remaining=285374)
[2026-06-08T09:03:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:13] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=283819)
[2026-06-08T09:03:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=148935)
[2026-06-08T09:03:15] Filtering fusions with <2 supporting reads (remaining=18907)
[2026-06-08T09:03:15] Filtering fusions with an e-value >=0.3 (remaining=5103)
[2026-06-08T09:03:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5140)
[2026-06-08T09:03:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5028)
[2026-06-08T09:03:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5029)
[2026-06-08T09:03:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4152)
[2026-06-08T09:03:25] Searching for fusions with spliced split reads (remaining=4214)
[2026-06-08T09:03:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=2978)
[2026-06-08T09:03:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2957)
[2026-06-08T09:03:31] Searching for fusions with >=4 spliced events (remaining=3342)
[2026-06-08T09:03:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1167)
[2026-06-08T09:03:46] Filtering fusions with anchors <=23nt (remaining=917)
[2026-06-08T09:03:46] Filtering end-to-end fusions with low support (remaining=886)
[2026-06-08T09:03:47] Filtering fusions with no coverage around the breakpoints (remaining=872)
[2026-06-08T09:03:47] Indexing gene sequences 
[2026-06-08T09:03:51] Filtering genes with >=30% identity (remaining=305)
[2026-06-08T09:03:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=130)
[2026-06-08T09:03:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=112)
[2026-06-08T09:03:55] Searching for additional isoforms (remaining=148)
[2026-06-08T09:03:56] Assigning confidence scores to events 
[2026-06-08T09:03:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:59] Writing fusions to file '659_ezg-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:04:00] Writing discarded fusions to file '659_ezg-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:22] Freeing resources
[2026-06-08T09:04:40] Done (elapsed time=00:11:22, CPU time=00:11:20, peak memory=15.4gb)