[2026-06-08T07:30:53] Launching Arriba 2.4.0
[2026-06-08T07:30:53] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:31:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:31:17] Reading chimeric alignments from '1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=914052)
[2026-06-08T07:31:39] Marking multi-mapping alignments (marked=715203)
[2026-06-08T07:31:39] Detecting strandedness (no)
[2026-06-08T07:31:39] Annotating alignments 
[2026-06-08T07:31:42] Filtering duplicates (remaining=312071)
[2026-06-08T07:31:43] 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=237970)
[2026-06-08T07:31:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=237970)
[2026-06-08T07:31:43] Filtering viral contigs with expression lower than the top 5 (remaining=237970)
[2026-06-08T07:31:43] Filtering viral contigs with less than 5% coverage (remaining=237970)
[2026-06-08T07:31:44] Estimating fragment length (mate gap mean=-66.0914, mate gap stddev=29.1907, read length mean=108.746)
[2026-06-08T07:31:44] Filtering read-through fragments with a distance <=10000bp (remaining=232613)
[2026-06-08T07:31:44] Filtering inconsistently clipped mates (remaining=225205)
[2026-06-08T07:31:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=218313)
[2026-06-08T07:31:45] Filtering fragments with small insert size (remaining=217947)
[2026-06-08T07:31:45] Filtering alignments with long gaps (remaining=217947)
[2026-06-08T07:31:45] Filtering fragments with both mates in the same gene (remaining=217821)
[2026-06-08T07:31:45] Filtering fusions arising from hairpin structures (remaining=205125)
[2026-06-08T07:31:45] Filtering reads with a mismatch p-value <=0.01 (remaining=70976)
[2026-06-08T07:31:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=14225)
[2026-06-08T07:31:46] Finding fusions and counting supporting reads (total=12066)
[2026-06-08T07:31:47] Merging adjacent fusion breakpoints (remaining=11956)
[2026-06-08T07:31:47] Filtering multi-mapping fusions by alignment score and read support (remaining=5069)
[2026-06-08T07:31:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:31:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=4925)
[2026-06-08T07:31:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=3191)
[2026-06-08T07:31:50] Filtering fusions with <2 supporting reads (remaining=149)
[2026-06-08T07:31:50] Filtering fusions with an e-value >=0.3 (remaining=76)
[2026-06-08T07:31:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=76)
[2026-06-08T07:31:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=63)
[2026-06-08T07:31:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=63)
[2026-06-08T07:31:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=58)
[2026-06-08T07:31:51] Searching for fusions with spliced split reads (remaining=61)
[2026-06-08T07:31:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=53)
[2026-06-08T07:31:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=53)
[2026-06-08T07:31:51] Searching for fusions with >=4 spliced events (remaining=53)
[2026-06-08T07:31:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14)
[2026-06-08T07:32:12] Filtering fusions with anchors <=23nt (remaining=14)
[2026-06-08T07:32:12] Filtering end-to-end fusions with low support (remaining=14)
[2026-06-08T07:32:12] Filtering fusions with no coverage around the breakpoints (remaining=13)
[2026-06-08T07:32:12] Indexing gene sequences 
[2026-06-08T07:32:13] Filtering genes with >=30% identity (remaining=10)
[2026-06-08T07:32:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-08T07:32:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:32:13] Searching for additional isoforms (remaining=0)
[2026-06-08T07:32:13] Assigning confidence scores to events 
[2026-06-08T07:32:13] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:32:13] Writing fusions to file '1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:32:13] Writing discarded fusions to file '1173_QEV_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:32:15] Freeing resources
[2026-06-08T07:32:17] Done (elapsed time=00:01:24, CPU time=00:01:23, peak memory=4.96gb)