[2026-06-08T07:59:20] Launching Arriba 2.4.0
[2026-06-08T07:59:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:59:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:59:42] Reading chimeric alignments from 'tih_rna_sample_00104_23H5VFLT4_s20.Aligned.sortedByCoord.out.bam' (total=14658658)
[2026-06-08T08:07:31] Marking multi-mapping alignments (marked=11319106)
[2026-06-08T08:07:37] Detecting strandedness (no)
[2026-06-08T08:07:37] Annotating alignments 
[2026-06-08T08:08:36] Filtering duplicates (remaining=5790737)
[2026-06-08T08:08:44] 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=5072572)
[2026-06-08T08:08:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5072572)
[2026-06-08T08:08:50] Filtering viral contigs with expression lower than the top 5 (remaining=5072572)
[2026-06-08T08:08:56] Filtering viral contigs with less than 5% coverage (remaining=5072572)
[2026-06-08T08:08:59] Estimating fragment length (mate gap mean=-76.6081, mate gap stddev=29.1294, read length mean=110.301)
[2026-06-08T08:09:00] Filtering read-through fragments with a distance <=10000bp (remaining=4905389)
[2026-06-08T08:09:03] Filtering inconsistently clipped mates (remaining=4767186)
[2026-06-08T08:09:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3939846)
[2026-06-08T08:09:11] Filtering fragments with small insert size (remaining=3935948)
[2026-06-08T08:09:14] Filtering alignments with long gaps (remaining=3935948)
[2026-06-08T08:09:17] Filtering fragments with both mates in the same gene (remaining=3934237)
[2026-06-08T08:09:21] Filtering fusions arising from hairpin structures (remaining=3673512)
[2026-06-08T08:09:24] Filtering reads with a mismatch p-value <=0.01 (remaining=908943)
[2026-06-08T08:09:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=580087)
[2026-06-08T08:09:42] Finding fusions and counting supporting reads (total=576515)
[2026-06-08T08:10:02] Merging adjacent fusion breakpoints (remaining=572883)
[2026-06-08T08:10:04] Filtering multi-mapping fusions by alignment score and read support (remaining=236881)
[2026-06-08T08:10:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:10:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=234348)
[2026-06-08T08:10:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=184678)
[2026-06-08T08:10:57] Filtering fusions with <2 supporting reads (remaining=7571)
[2026-06-08T08:10:58] Filtering fusions with an e-value >=0.3 (remaining=1440)
[2026-06-08T08:10:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1466)
[2026-06-08T08:11:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1225)
[2026-06-08T08:11:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1225)
[2026-06-08T08:11:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1224)
[2026-06-08T08:11:12] Searching for fusions with spliced split reads (remaining=1312)
[2026-06-08T08:11:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=990)
[2026-06-08T08:11:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=972)
[2026-06-08T08:11:20] Searching for fusions with >=4 spliced events (remaining=1059)
[2026-06-08T08:11:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=357)
[2026-06-08T08:11:37] Filtering fusions with anchors <=23nt (remaining=283)
[2026-06-08T08:11:38] Filtering end-to-end fusions with low support (remaining=276)
[2026-06-08T08:11:39] Filtering fusions with no coverage around the breakpoints (remaining=273)
[2026-06-08T08:11:40] Indexing gene sequences 
[2026-06-08T08:11:42] Filtering genes with >=30% identity (remaining=105)
[2026-06-08T08:11:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=47)
[2026-06-08T08:11:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=40)
[2026-06-08T08:11:47] Searching for additional isoforms (remaining=46)
[2026-06-08T08:11:48] Assigning confidence scores to events 
[2026-06-08T08:11:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:11:53] Writing fusions to file 'tih_rna_sample_00104_23H5VFLT4_s20.arriba.fusions.tsv' 
[2026-06-08T08:11:54] Writing discarded fusions to file 'tih_rna_sample_00104_23H5VFLT4_s20.arriba.fusions.discarded.tsv'
[2026-06-08T08:12:23] Freeing resources
[2026-06-08T08:12:46] Done (elapsed time=00:13:26, CPU time=00:13:24, peak memory=20.1gb)