[2026-06-08T07:29:52] Launching Arriba 2.4.0
[2026-06-08T07:29:52] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:30:02] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:30:07] Reading chimeric alignments from '1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=692597)
[2026-06-08T07:30:33] Marking multi-mapping alignments (marked=478867)
[2026-06-08T07:30:33] Detecting strandedness (reverse)
[2026-06-08T07:30:33] Assigning strands to alignments 
[2026-06-08T07:30:34] Annotating alignments 
[2026-06-08T07:30:36] Filtering duplicates (remaining=594691)
[2026-06-08T07:30:37] 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=537150)
[2026-06-08T07:30:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=537150)
[2026-06-08T07:30:37] Filtering viral contigs with expression lower than the top 5 (remaining=537150)
[2026-06-08T07:30:38] Filtering viral contigs with less than 5% coverage (remaining=537150)
[2026-06-08T07:30:38] Estimating fragment length (mate gap mean=-81.7819, mate gap stddev=27.442, read length mean=120.513)
[2026-06-08T07:30:38] Filtering read-through fragments with a distance <=10000bp (remaining=514063)
[2026-06-08T07:30:38] Filtering inconsistently clipped mates (remaining=507273)
[2026-06-08T07:30:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=498115)
[2026-06-08T07:30:39] Filtering fragments with small insert size (remaining=498038)
[2026-06-08T07:30:39] Filtering alignments with long gaps (remaining=498038)
[2026-06-08T07:30:39] Filtering fragments with both mates in the same gene (remaining=497925)
[2026-06-08T07:30:39] Filtering fusions arising from hairpin structures (remaining=479103)
[2026-06-08T07:30:39] Filtering reads with a mismatch p-value <=0.01 (remaining=242654)
[2026-06-08T07:30:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=101142)
[2026-06-08T07:30:41] Finding fusions and counting supporting reads (total=97597)
[2026-06-08T07:30:43] Merging adjacent fusion breakpoints (remaining=97304)
[2026-06-08T07:30:43] Filtering multi-mapping fusions by alignment score and read support (remaining=53154)
[2026-06-08T07:30:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:30:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=52940)
[2026-06-08T07:30:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=42432)
[2026-06-08T07:30:46] Filtering fusions with <2 supporting reads (remaining=1640)
[2026-06-08T07:30:46] Filtering fusions with an e-value >=0.3 (remaining=729)
[2026-06-08T07:30:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=753)
[2026-06-08T07:30:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=752)
[2026-06-08T07:30:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=752)
[2026-06-08T07:30:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=724)
[2026-06-08T07:30:48] Searching for fusions with spliced split reads (remaining=741)
[2026-06-08T07:30:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=613)
[2026-06-08T07:30:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=606)
[2026-06-08T07:30:48] Searching for fusions with >=4 spliced events (remaining=610)
[2026-06-08T07:30:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=158)
[2026-06-08T07:31:02] Filtering fusions with anchors <=23nt (remaining=125)
[2026-06-08T07:31:02] Filtering end-to-end fusions with low support (remaining=122)
[2026-06-08T07:31:02] Filtering fusions with no coverage around the breakpoints (remaining=117)
[2026-06-08T07:31:02] Indexing gene sequences 
[2026-06-08T07:31:03] Filtering genes with >=30% identity (remaining=85)
[2026-06-08T07:31:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=77)
[2026-06-08T07:31:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=77)
[2026-06-08T07:31:04] Searching for additional isoforms (remaining=82)
[2026-06-08T07:31:04] Assigning confidence scores to events 
[2026-06-08T07:31:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:31:04] Writing fusions to file '1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:31:04] Writing discarded fusions to file '1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:31:07] Freeing resources
[2026-06-08T07:31:10] Done (elapsed time=00:01:18, CPU time=00:01:17, peak memory=4.83gb)