[2026-06-08T08:21:41] Launching Arriba 2.4.0
[2026-06-08T08:21:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:22:04] Reading chimeric alignments from 'tih_rna_sample_00402_23H5VFLT4_s28.Aligned.sortedByCoord.out.bam' (total=10554386)
[2026-06-08T08:30:35] Marking multi-mapping alignments (marked=6940163)
[2026-06-08T08:30:40] Detecting strandedness (reverse)
[2026-06-08T08:30:40] Assigning strands to alignments 
[2026-06-08T08:30:42] Annotating alignments 
[2026-06-08T08:31:18] Filtering duplicates (remaining=7225961)
[2026-06-08T08:31:25] 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=6837869)
[2026-06-08T08:31:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6837869)
[2026-06-08T08:31:29] Filtering viral contigs with expression lower than the top 5 (remaining=6837869)
[2026-06-08T08:31:34] Filtering viral contigs with less than 5% coverage (remaining=6837869)
[2026-06-08T08:31:36] Estimating fragment length (mate gap mean=-86.8277, mate gap stddev=29.3766, read length mean=129.79)
[2026-06-08T08:31:37] Filtering read-through fragments with a distance <=10000bp (remaining=6221669)
[2026-06-08T08:31:39] Filtering inconsistently clipped mates (remaining=6087215)
[2026-06-08T08:31:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5663976)
[2026-06-08T08:31:46] Filtering fragments with small insert size (remaining=5662391)
[2026-06-08T08:31:48] Filtering alignments with long gaps (remaining=5662391)
[2026-06-08T08:31:51] Filtering fragments with both mates in the same gene (remaining=5660804)
[2026-06-08T08:31:53] Filtering fusions arising from hairpin structures (remaining=5175159)
[2026-06-08T08:31:55] Filtering reads with a mismatch p-value <=0.01 (remaining=2294309)
[2026-06-08T08:32:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=1603137)
[2026-06-08T08:32:24] Finding fusions and counting supporting reads (total=1292462)
[2026-06-08T08:32:42] Merging adjacent fusion breakpoints (remaining=1281421)
[2026-06-08T08:32:45] Filtering multi-mapping fusions by alignment score and read support (remaining=751302)
[2026-06-08T08:33:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=749071)
[2026-06-08T08:33:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=485153)
[2026-06-08T08:33:28] Filtering fusions with <2 supporting reads (remaining=37389)
[2026-06-08T08:33:29] Filtering fusions with an e-value >=0.3 (remaining=7962)
[2026-06-08T08:33:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8016)
[2026-06-08T08:33:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7784)
[2026-06-08T08:33:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7784)
[2026-06-08T08:33:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6609)
[2026-06-08T08:33:42] Searching for fusions with spliced split reads (remaining=6744)
[2026-06-08T08:33:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=4162)
[2026-06-08T08:33:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4118)
[2026-06-08T08:33:50] Searching for fusions with >=4 spliced events (remaining=5254)
[2026-06-08T08:33:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2311)
[2026-06-08T08:34:08] Filtering fusions with anchors <=23nt (remaining=1922)
[2026-06-08T08:34:08] Filtering end-to-end fusions with low support (remaining=1891)
[2026-06-08T08:34:09] Filtering fusions with no coverage around the breakpoints (remaining=1869)
[2026-06-08T08:34:10] Indexing gene sequences 
[2026-06-08T08:34:17] Filtering genes with >=30% identity (remaining=514)
[2026-06-08T08:34:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=210)
[2026-06-08T08:34:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=178)
[2026-06-08T08:34:27] Searching for additional isoforms (remaining=248)
[2026-06-08T08:34:28] Assigning confidence scores to events 
[2026-06-08T08:34:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:33] Writing fusions to file 'tih_rna_sample_00402_23H5VFLT4_s28.arriba.fusions.tsv' 
[2026-06-08T08:34:37] Writing discarded fusions to file 'tih_rna_sample_00402_23H5VFLT4_s28.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:16] Freeing resources
[2026-06-08T08:35:35] Done (elapsed time=00:13:54, CPU time=00:13:53, peak memory=16gb)