[2026-06-04T21:14:49] Launching Arriba 2.4.0
[2026-06-04T21:14:49] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:14:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:15:00] Reading chimeric alignments from '659_ezg-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10050757)
[2026-06-04T21:21:29] Marking multi-mapping alignments (marked=6289292)
[2026-06-04T21:21:33] Detecting strandedness (reverse)
[2026-06-04T21:21:33] Assigning strands to alignments 
[2026-06-04T21:21:35] Annotating alignments 
[2026-06-04T21:22:05] Filtering duplicates (remaining=6255652)
[2026-06-04T21:22:12] 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)
[2026-06-04T21:22:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5952842)
[2026-06-04T21:22:16] Filtering viral contigs with expression lower than the top 5 (remaining=5952842)
[2026-06-04T21:22:20] Filtering viral contigs with less than 5% coverage (remaining=5952842)
[2026-06-04T21:22:22] Estimating fragment length (mate gap mean=-87.7606, mate gap stddev=28.1147, read length mean=130.476)
[2026-06-04T21:22:22] Filtering read-through fragments with a distance <=10000bp (remaining=5524540)
[2026-06-04T21:22:24] Filtering inconsistently clipped mates (remaining=5434808)
[2026-06-04T21:22:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5295803)
[2026-06-04T21:22:30] Filtering fragments with small insert size (remaining=5294993)
[2026-06-04T21:22:32] Filtering alignments with long gaps (remaining=5294993)
[2026-06-04T21:22:34] Filtering fragments with both mates in the same gene (remaining=5294049)
[2026-06-04T21:22:36] Filtering fusions arising from hairpin structures (remaining=4986573)
[2026-06-04T21:22:39] Filtering reads with a mismatch p-value <=0.01 (remaining=2651980)
[2026-06-04T21:22:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1213677)
[2026-06-04T21:23:01] Finding fusions and counting supporting reads (total=865792)
[2026-06-04T21:23:16] Merging adjacent fusion breakpoints (remaining=855346)
[2026-06-04T21:23:17] Filtering multi-mapping fusions by alignment score and read support (remaining=540265)
[2026-06-04T21:23:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:23:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=538477)
[2026-06-04T21:23:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=284174)
[2026-06-04T21:23:54] Filtering fusions with <2 supporting reads (remaining=39395)
[2026-06-04T21:23:55] Filtering fusions with an e-value >=0.3 (remaining=9498)
[2026-06-04T21:23:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9557)
[2026-06-04T21:23:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9437)
[2026-06-04T21:23:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9440)
[2026-06-04T21:24:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7880)
[2026-06-04T21:24:05] Searching for fusions with spliced split reads (remaining=7890)
[2026-06-04T21:24:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=5029)
[2026-06-04T21:24:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4984)
[2026-06-04T21:24:12] Searching for fusions with >=4 spliced events (remaining=6153)
[2026-06-04T21:24:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2380)
[2026-06-04T21:24:27] Filtering fusions with anchors <=23nt (remaining=1908)
[2026-06-04T21:24:27] Filtering end-to-end fusions with low support (remaining=1860)
[2026-06-04T21:24:28] Filtering fusions with no coverage around the breakpoints (remaining=1821)
[2026-06-04T21:24:29] Indexing gene sequences 
[2026-06-04T21:24:34] Filtering genes with >=30% identity (remaining=556)
[2026-06-04T21:24:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=243)
[2026-06-04T21:24:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=190)
[2026-06-04T21:24:40] Searching for additional isoforms (remaining=272)
[2026-06-04T21:24:42] Assigning confidence scores to events 
[2026-06-04T21:24:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:24:45] Writing fusions to file '659_ezg-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:24:47] Writing discarded fusions to file '659_ezg-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:25:12] Freeing resources
[2026-06-04T21:25:28] Done (elapsed time=00:10:39, CPU time=00:10:37, peak memory=14.8gb)