[2026-06-08T08:31:36] Launching Arriba 2.4.0
[2026-06-08T08:31:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:52] Reading chimeric alignments from 'tih_rna_sample_00163_23H5VFLT4_s43.Aligned.sortedByCoord.out.bam' (total=8476727)
[2026-06-08T08:38:21] Marking multi-mapping alignments (marked=5391595)
[2026-06-08T08:38:24] Detecting strandedness (reverse)
[2026-06-08T08:38:24] Assigning strands to alignments 
[2026-06-08T08:38:26] Annotating alignments 
[2026-06-08T08:38:51] Filtering duplicates (remaining=5568784)
[2026-06-08T08:38:56] 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=5271916)
[2026-06-08T08:38:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5271916)
[2026-06-08T08:38:59] Filtering viral contigs with expression lower than the top 5 (remaining=5271916)
[2026-06-08T08:39:03] Filtering viral contigs with less than 5% coverage (remaining=5271916)
[2026-06-08T08:39:04] Estimating fragment length (mate gap mean=-84.8045, mate gap stddev=29.7106, read length mean=128.433)
[2026-06-08T08:39:05] Filtering read-through fragments with a distance <=10000bp (remaining=4908334)
[2026-06-08T08:39:06] Filtering inconsistently clipped mates (remaining=4801658)
[2026-06-08T08:39:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4409368)
[2026-06-08T08:39:11] Filtering fragments with small insert size (remaining=4408109)
[2026-06-08T08:39:13] Filtering alignments with long gaps (remaining=4408109)
[2026-06-08T08:39:14] Filtering fragments with both mates in the same gene (remaining=4406571)
[2026-06-08T08:39:16] Filtering fusions arising from hairpin structures (remaining=4069852)
[2026-06-08T08:39:18] Filtering reads with a mismatch p-value <=0.01 (remaining=1867632)
[2026-06-08T08:39:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=1158262)
[2026-06-08T08:39:37] Finding fusions and counting supporting reads (total=940710)
[2026-06-08T08:39:50] Merging adjacent fusion breakpoints (remaining=935622)
[2026-06-08T08:39:51] Filtering multi-mapping fusions by alignment score and read support (remaining=555434)
[2026-06-08T08:40:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=553023)
[2026-06-08T08:40:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=362660)
[2026-06-08T08:40:22] Filtering fusions with <2 supporting reads (remaining=32974)
[2026-06-08T08:40:23] Filtering fusions with an e-value >=0.3 (remaining=8512)
[2026-06-08T08:40:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8567)
[2026-06-08T08:40:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8365)
[2026-06-08T08:40:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8366)
[2026-06-08T08:40:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6173)
[2026-06-08T08:40:32] Searching for fusions with spliced split reads (remaining=6296)
[2026-06-08T08:40:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=4043)
[2026-06-08T08:40:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3996)
[2026-06-08T08:40:38] Searching for fusions with >=4 spliced events (remaining=4799)
[2026-06-08T08:40:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1898)
[2026-06-08T08:40:53] Filtering fusions with anchors <=23nt (remaining=1543)
[2026-06-08T08:40:54] Filtering end-to-end fusions with low support (remaining=1505)
[2026-06-08T08:40:54] Filtering fusions with no coverage around the breakpoints (remaining=1485)
[2026-06-08T08:40:55] Indexing gene sequences 
[2026-06-08T08:41:01] Filtering genes with >=30% identity (remaining=451)
[2026-06-08T08:41:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=206)
[2026-06-08T08:41:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=190)
[2026-06-08T08:41:19] Searching for additional isoforms (remaining=264)
[2026-06-08T08:41:21] Assigning confidence scores to events 
[2026-06-08T08:41:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:24] Writing fusions to file 'tih_rna_sample_00163_23H5VFLT4_s43.arriba.fusions.tsv' 
[2026-06-08T08:41:26] Writing discarded fusions to file 'tih_rna_sample_00163_23H5VFLT4_s43.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:51] Freeing resources
[2026-06-08T08:42:05] Done (elapsed time=00:10:29, CPU time=00:10:28, peak memory=13.5gb)