[2026-06-08T09:02:33] Launching Arriba 2.4.0
[2026-06-08T09:02:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:02:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:02:49] Reading chimeric alignments from '1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=11824913)
[2026-06-08T09:09:59] Marking multi-mapping alignments (marked=7383171)
[2026-06-08T09:10:04] Detecting strandedness (reverse)
[2026-06-08T09:10:04] Assigning strands to alignments 
[2026-06-08T09:10:07] Annotating alignments 
[2026-06-08T09:10:48] Filtering duplicates (remaining=9242168)
[2026-06-08T09:10:57] 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=8696439)
[2026-06-08T09:11:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8696439)
[2026-06-08T09:11:02] Filtering viral contigs with expression lower than the top 5 (remaining=8696439)
[2026-06-08T09:11:08] Filtering viral contigs with less than 5% coverage (remaining=8696439)
[2026-06-08T09:11:11] Estimating fragment length (mate gap mean=-83.3581, mate gap stddev=28.3667, read length mean=131.948)
[2026-06-08T09:11:11] Filtering read-through fragments with a distance <=10000bp (remaining=8389760)
[2026-06-08T09:11:13] Filtering inconsistently clipped mates (remaining=8297464)
[2026-06-08T09:11:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8153811)
[2026-06-08T09:11:21] Filtering fragments with small insert size (remaining=8152999)
[2026-06-08T09:11:24] Filtering alignments with long gaps (remaining=8152999)
[2026-06-08T09:11:26] Filtering fragments with both mates in the same gene (remaining=8151736)
[2026-06-08T09:11:29] Filtering fusions arising from hairpin structures (remaining=7885191)
[2026-06-08T09:11:32] Filtering reads with a mismatch p-value <=0.01 (remaining=4392346)
[2026-06-08T09:11:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=2219797)
[2026-06-08T09:12:09] Finding fusions and counting supporting reads (total=2006258)
[2026-06-08T09:12:33] Merging adjacent fusion breakpoints (remaining=1999857)
[2026-06-08T09:12:36] Filtering multi-mapping fusions by alignment score and read support (remaining=1238766)
[2026-06-08T09:13:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:13:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1237721)
[2026-06-08T09:13:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1080123)
[2026-06-08T09:13:29] Filtering fusions with <2 supporting reads (remaining=32516)
[2026-06-08T09:13:30] Filtering fusions with an e-value >=0.3 (remaining=4731)
[2026-06-08T09:13:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4786)
[2026-06-08T09:13:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4738)
[2026-06-08T09:13:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4738)
[2026-06-08T09:13:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4658)
[2026-06-08T09:13:47] Searching for fusions with spliced split reads (remaining=4694)
[2026-06-08T09:13:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=3249)
[2026-06-08T09:13:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3209)
[2026-06-08T09:13:58] Searching for fusions with >=4 spliced events (remaining=4188)
[2026-06-08T09:14:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1869)
[2026-06-08T09:14:13] Filtering fusions with anchors <=23nt (remaining=1545)
[2026-06-08T09:14:14] Filtering end-to-end fusions with low support (remaining=1515)
[2026-06-08T09:14:15] Filtering fusions with no coverage around the breakpoints (remaining=1489)
[2026-06-08T09:14:16] Indexing gene sequences 
[2026-06-08T09:14:23] Filtering genes with >=30% identity (remaining=586)
[2026-06-08T09:14:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=414)
[2026-06-08T09:14:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=251)
[2026-06-08T09:14:35] Searching for additional isoforms (remaining=372)
[2026-06-08T09:14:37] Assigning confidence scores to events 
[2026-06-08T09:14:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:14:43] Writing fusions to file '1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:14:47] Writing discarded fusions to file '1173_NWE_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:15:37] Freeing resources
[2026-06-08T09:15:59] Done (elapsed time=00:13:26, CPU time=00:13:23, peak memory=16.5gb)