[2026-06-08T08:33:50] Launching Arriba 2.4.0
[2026-06-08T08:33:50] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:09] Reading chimeric alignments from '659_ezg-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10050757)
[2026-06-08T08:43:05] Marking multi-mapping alignments (marked=6289292)
[2026-06-08T08:43:10] Detecting strandedness (reverse)
[2026-06-08T08:43:10] Assigning strands to alignments 
[2026-06-08T08:43:13] Annotating alignments 
[2026-06-08T08:43:56] Filtering duplicates (remaining=6255652)
[2026-06-08T08:44:08] 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=5952842)
[2026-06-08T08:44:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5952842)
[2026-06-08T08:44:12] Filtering viral contigs with expression lower than the top 5 (remaining=5952842)
[2026-06-08T08:44:18] Filtering viral contigs with less than 5% coverage (remaining=5952842)
[2026-06-08T08:44:21] Estimating fragment length (mate gap mean=-87.7606, mate gap stddev=28.1147, read length mean=130.476)
[2026-06-08T08:44:21] Filtering read-through fragments with a distance <=10000bp (remaining=5524540)
[2026-06-08T08:44:23] Filtering inconsistently clipped mates (remaining=5434808)
[2026-06-08T08:44:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5295803)
[2026-06-08T08:44:31] Filtering fragments with small insert size (remaining=5294993)
[2026-06-08T08:44:33] Filtering alignments with long gaps (remaining=5294993)
[2026-06-08T08:44:35] Filtering fragments with both mates in the same gene (remaining=5294049)
[2026-06-08T08:44:38] Filtering fusions arising from hairpin structures (remaining=4986573)
[2026-06-08T08:44:41] Filtering reads with a mismatch p-value <=0.01 (remaining=2651980)
[2026-06-08T08:44:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=1213677)
[2026-06-08T08:45:10] Finding fusions and counting supporting reads (total=865792)
[2026-06-08T08:45:32] Merging adjacent fusion breakpoints (remaining=855346)
[2026-06-08T08:45:33] Filtering multi-mapping fusions by alignment score and read support (remaining=540265)
[2026-06-08T08:46:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=538477)
[2026-06-08T08:46:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=284174)
[2026-06-08T08:46:26] Filtering fusions with <2 supporting reads (remaining=39395)
[2026-06-08T08:46:26] Filtering fusions with an e-value >=0.3 (remaining=9498)
[2026-06-08T08:46:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9557)
[2026-06-08T08:46:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9437)
[2026-06-08T08:46:32] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9440)
[2026-06-08T08:46:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7880)
[2026-06-08T08:46:40] Searching for fusions with spliced split reads (remaining=7890)
[2026-06-08T08:46:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=5029)
[2026-06-08T08:46:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4984)
[2026-06-08T08:46:49] Searching for fusions with >=4 spliced events (remaining=6153)
[2026-06-08T08:46:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2380)
[2026-06-08T08:47:14] Filtering fusions with anchors <=23nt (remaining=1908)
[2026-06-08T08:47:15] Filtering end-to-end fusions with low support (remaining=1860)
[2026-06-08T08:47:16] Filtering fusions with no coverage around the breakpoints (remaining=1821)
[2026-06-08T08:47:17] Indexing gene sequences 
[2026-06-08T08:47:28] Filtering genes with >=30% identity (remaining=556)
[2026-06-08T08:47:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=243)
[2026-06-08T08:47:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=190)
[2026-06-08T08:47:38] Searching for additional isoforms (remaining=272)
[2026-06-08T08:47:41] Assigning confidence scores to events 
[2026-06-08T08:47:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:48] Writing fusions to file '659_ezg-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:52] Writing discarded fusions to file '659_ezg-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:55] Freeing resources
[2026-06-08T08:49:32] Done (elapsed time=00:15:42, CPU time=00:15:40, peak memory=14.8gb)