[2026-06-08T07:32:50] Launching Arriba 2.4.0
[2026-06-08T07:32:50] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:33:02] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:33:07] Reading chimeric alignments from '1173_RPC_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=1157682)
[2026-06-08T07:33:52] Marking multi-mapping alignments (marked=816851)
[2026-06-08T07:33:53] Detecting strandedness (reverse)
[2026-06-08T07:33:53] Assigning strands to alignments 
[2026-06-08T07:33:53] Annotating alignments 
[2026-06-08T07:33:57] Filtering duplicates (remaining=973464)
[2026-06-08T07:33:58] 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=876536)
[2026-06-08T07:33:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=876536)
[2026-06-08T07:33:59] Filtering viral contigs with expression lower than the top 5 (remaining=876536)
[2026-06-08T07:33:59] Filtering viral contigs with less than 5% coverage (remaining=876536)
[2026-06-08T07:34:00] Estimating fragment length (mate gap mean=-77.9551, mate gap stddev=26.2921, read length mean=112.897)
[2026-06-08T07:34:00] Filtering read-through fragments with a distance <=10000bp (remaining=850201)
[2026-06-08T07:34:00] Filtering inconsistently clipped mates (remaining=839638)
[2026-06-08T07:34:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=823092)
[2026-06-08T07:34:01] Filtering fragments with small insert size (remaining=822905)
[2026-06-08T07:34:01] Filtering alignments with long gaps (remaining=822905)
[2026-06-08T07:34:01] Filtering fragments with both mates in the same gene (remaining=822667)
[2026-06-08T07:34:01] Filtering fusions arising from hairpin structures (remaining=798650)
[2026-06-08T07:34:02] Filtering reads with a mismatch p-value <=0.01 (remaining=363470)
[2026-06-08T07:34:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=134402)
[2026-06-08T07:34:05] Finding fusions and counting supporting reads (total=129919)
[2026-06-08T07:34:07] Merging adjacent fusion breakpoints (remaining=129445)
[2026-06-08T07:34:07] Filtering multi-mapping fusions by alignment score and read support (remaining=69655)
[2026-06-08T07:34:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:34:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=69473)
[2026-06-08T07:34:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=58845)
[2026-06-08T07:34:12] Filtering fusions with <2 supporting reads (remaining=2043)
[2026-06-08T07:34:12] Filtering fusions with an e-value >=0.3 (remaining=640)
[2026-06-08T07:34:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=654)
[2026-06-08T07:34:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=650)
[2026-06-08T07:34:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=650)
[2026-06-08T07:34:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=647)
[2026-06-08T07:34:14] Searching for fusions with spliced split reads (remaining=668)
[2026-06-08T07:34:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=556)
[2026-06-08T07:34:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=551)
[2026-06-08T07:34:15] Searching for fusions with >=4 spliced events (remaining=564)
[2026-06-08T07:34:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=237)
[2026-06-08T07:34:26] Filtering fusions with anchors <=23nt (remaining=181)
[2026-06-08T07:34:26] Filtering end-to-end fusions with low support (remaining=174)
[2026-06-08T07:34:26] Filtering fusions with no coverage around the breakpoints (remaining=168)
[2026-06-08T07:34:26] Indexing gene sequences 
[2026-06-08T07:34:28] Filtering genes with >=30% identity (remaining=88)
[2026-06-08T07:34:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=68)
[2026-06-08T07:34:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=68)
[2026-06-08T07:34:29] Searching for additional isoforms (remaining=71)
[2026-06-08T07:34:29] Assigning confidence scores to events 
[2026-06-08T07:34:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:34:30] Writing fusions to file '1173_RPC_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:34:30] Writing discarded fusions to file '1173_RPC_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:34:36] Freeing resources
[2026-06-08T07:34:39] Done (elapsed time=00:01:49, CPU time=00:01:47, peak memory=5.3gb)