[2026-06-08T08:45:19] Launching Arriba 2.4.0
[2026-06-08T08:45:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:27] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:32] Reading chimeric alignments from 'tih_rna_sample_00161_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10134155)
[2026-06-08T08:51:53] Marking multi-mapping alignments (marked=6514093)
[2026-06-08T08:51:57] Detecting strandedness (reverse)
[2026-06-08T08:51:57] Assigning strands to alignments 
[2026-06-08T08:51:59] Annotating alignments 
[2026-06-08T08:52:30] Filtering duplicates (remaining=3558176)
[2026-06-08T08:52:34] 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=3349551)
[2026-06-08T08:52:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3349551)
[2026-06-08T08:52:38] Filtering viral contigs with expression lower than the top 5 (remaining=3349551)
[2026-06-08T08:52:42] Filtering viral contigs with less than 5% coverage (remaining=3349551)
[2026-06-08T08:52:44] Estimating fragment length (mate gap mean=-87.7696, mate gap stddev=27.4832, read length mean=129.341)
[2026-06-08T08:52:44] Filtering read-through fragments with a distance <=10000bp (remaining=3147648)
[2026-06-08T08:52:46] Filtering inconsistently clipped mates (remaining=3092530)
[2026-06-08T08:52:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2994410)
[2026-06-08T08:52:50] Filtering fragments with small insert size (remaining=2993798)
[2026-06-08T08:52:52] Filtering alignments with long gaps (remaining=2993798)
[2026-06-08T08:52:54] Filtering fragments with both mates in the same gene (remaining=2993120)
[2026-06-08T08:52:56] Filtering fusions arising from hairpin structures (remaining=2859793)
[2026-06-08T08:52:58] Filtering reads with a mismatch p-value <=0.01 (remaining=1126106)
[2026-06-08T08:53:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=465264)
[2026-06-08T08:53:12] Finding fusions and counting supporting reads (total=397589)
[2026-06-08T08:53:25] Merging adjacent fusion breakpoints (remaining=394609)
[2026-06-08T08:53:26] Filtering multi-mapping fusions by alignment score and read support (remaining=236942)
[2026-06-08T08:53:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=235630)
[2026-06-08T08:53:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=124110)
[2026-06-08T08:53:59] Filtering fusions with <2 supporting reads (remaining=13268)
[2026-06-08T08:53:59] Filtering fusions with an e-value >=0.3 (remaining=3275)
[2026-06-08T08:54:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3307)
[2026-06-08T08:54:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3253)
[2026-06-08T08:54:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3253)
[2026-06-08T08:54:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3015)
[2026-06-08T08:54:08] Searching for fusions with spliced split reads (remaining=3085)
[2026-06-08T08:54:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=2302)
[2026-06-08T08:54:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2272)
[2026-06-08T08:54:13] Searching for fusions with >=4 spliced events (remaining=2655)
[2026-06-08T08:54:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1142)
[2026-06-08T08:54:26] Filtering fusions with anchors <=23nt (remaining=1001)
[2026-06-08T08:54:26] Filtering end-to-end fusions with low support (remaining=982)
[2026-06-08T08:54:26] Filtering fusions with no coverage around the breakpoints (remaining=957)
[2026-06-08T08:54:27] Indexing gene sequences 
[2026-06-08T08:54:33] Filtering genes with >=30% identity (remaining=456)
[2026-06-08T08:54:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=321)
[2026-06-08T08:54:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=253)
[2026-06-08T08:54:41] Searching for additional isoforms (remaining=305)
[2026-06-08T08:54:42] Assigning confidence scores to events 
[2026-06-08T08:54:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:44] Writing fusions to file 'tih_rna_sample_00161_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:46] Writing discarded fusions to file 'tih_rna_sample_00161_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:03] Freeing resources
[2026-06-08T08:55:19] Done (elapsed time=00:10:00, CPU time=00:09:58, peak memory=14.6gb)