[2026-06-08T08:25:27] Launching Arriba 2.4.0
[2026-06-08T08:25:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:43] Reading chimeric alignments from '1173_NFO_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=18620842)
[2026-06-08T08:32:47] Marking multi-mapping alignments (marked=13696931)
[2026-06-08T08:32:55] Detecting strandedness (no)
[2026-06-08T08:32:55] Annotating alignments 
[2026-06-08T08:33:55] Filtering duplicates (remaining=6700759)
[2026-06-08T08:34:04] 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=5935319)
[2026-06-08T08:34:08] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5935319)
[2026-06-08T08:34:12] Filtering viral contigs with expression lower than the top 5 (remaining=5935319)
[2026-06-08T08:34:20] Filtering viral contigs with less than 5% coverage (remaining=5935319)
[2026-06-08T08:34:24] Estimating fragment length (mate gap mean=-74.1657, mate gap stddev=26.7723, read length mean=110.608)
[2026-06-08T08:34:24] Filtering read-through fragments with a distance <=10000bp (remaining=5817378)
[2026-06-08T08:34:28] Filtering inconsistently clipped mates (remaining=5664688)
[2026-06-08T08:34:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5499379)
[2026-06-08T08:34:37] Filtering fragments with small insert size (remaining=5496697)
[2026-06-08T08:34:41] Filtering alignments with long gaps (remaining=5496697)
[2026-06-08T08:34:45] Filtering fragments with both mates in the same gene (remaining=5495148)
[2026-06-08T08:34:48] Filtering fusions arising from hairpin structures (remaining=5148190)
[2026-06-08T08:34:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2061600)
[2026-06-08T08:35:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=721565)
[2026-06-08T08:35:18] Finding fusions and counting supporting reads (total=640381)
[2026-06-08T08:35:39] Merging adjacent fusion breakpoints (remaining=633431)
[2026-06-08T08:35:41] Filtering multi-mapping fusions by alignment score and read support (remaining=316981)
[2026-06-08T08:36:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=315773)
[2026-06-08T08:36:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=242862)
[2026-06-08T08:36:38] Filtering fusions with <2 supporting reads (remaining=10453)
[2026-06-08T08:36:39] Filtering fusions with an e-value >=0.3 (remaining=2383)
[2026-06-08T08:36:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2494)
[2026-06-08T08:36:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2348)
[2026-06-08T08:36:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2348)
[2026-06-08T08:36:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2348)
[2026-06-08T08:36:54] Searching for fusions with spliced split reads (remaining=2491)
[2026-06-08T08:37:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=1822)
[2026-06-08T08:37:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1802)
[2026-06-08T08:37:03] Searching for fusions with >=4 spliced events (remaining=1968)
[2026-06-08T08:37:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=787)
[2026-06-08T08:37:18] Filtering fusions with anchors <=23nt (remaining=655)
[2026-06-08T08:37:19] Filtering end-to-end fusions with low support (remaining=620)
[2026-06-08T08:37:20] Filtering fusions with no coverage around the breakpoints (remaining=596)
[2026-06-08T08:37:21] Indexing gene sequences 
[2026-06-08T08:37:25] Filtering genes with >=30% identity (remaining=183)
[2026-06-08T08:37:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=88)
[2026-06-08T08:37:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=88)
[2026-06-08T08:37:30] Searching for additional isoforms (remaining=101)
[2026-06-08T08:37:31] Assigning confidence scores to events 
[2026-06-08T08:37:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:34] Writing fusions to file '1173_NFO_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:37:36] Writing discarded fusions to file '1173_NFO_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:02] Freeing resources
[2026-06-08T08:38:28] Done (elapsed time=00:13:01, CPU time=00:13:00, peak memory=22.7gb)