[2026-06-08T08:46:40] Launching Arriba 2.4.0
[2026-06-08T08:46:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:00] Reading chimeric alignments from 'tih_rna_sample_00161_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=10611146)
[2026-06-08T08:55:05] Marking multi-mapping alignments (marked=6838461)
[2026-06-08T08:55:10] Detecting strandedness (reverse)
[2026-06-08T08:55:10] Assigning strands to alignments 
[2026-06-08T08:55:12] Annotating alignments 
[2026-06-08T08:55:50] Filtering duplicates (remaining=4593456)
[2026-06-08T08:55:57] 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=4329539)
[2026-06-08T08:55:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4329539)
[2026-06-08T08:56:01] Filtering viral contigs with expression lower than the top 5 (remaining=4329539)
[2026-06-08T08:56:06] Filtering viral contigs with less than 5% coverage (remaining=4329539)
[2026-06-08T08:56:09] Estimating fragment length (mate gap mean=-88.8436, mate gap stddev=27.4251, read length mean=131.157)
[2026-06-08T08:56:09] Filtering read-through fragments with a distance <=10000bp (remaining=4026578)
[2026-06-08T08:56:11] Filtering inconsistently clipped mates (remaining=3961640)
[2026-06-08T08:56:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3847279)
[2026-06-08T08:56:18] Filtering fragments with small insert size (remaining=3846569)
[2026-06-08T08:56:20] Filtering alignments with long gaps (remaining=3846569)
[2026-06-08T08:56:23] Filtering fragments with both mates in the same gene (remaining=3845853)
[2026-06-08T08:56:25] Filtering fusions arising from hairpin structures (remaining=3657702)
[2026-06-08T08:56:28] Filtering reads with a mismatch p-value <=0.01 (remaining=1502877)
[2026-06-08T08:56:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=672296)
[2026-06-08T08:56:47] Finding fusions and counting supporting reads (total=559653)
[2026-06-08T08:57:04] Merging adjacent fusion breakpoints (remaining=554779)
[2026-06-08T08:57:05] Filtering multi-mapping fusions by alignment score and read support (remaining=335487)
[2026-06-08T08:57:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=333654)
[2026-06-08T08:57:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=176452)
[2026-06-08T08:57:48] Filtering fusions with <2 supporting reads (remaining=20513)
[2026-06-08T08:57:49] Filtering fusions with an e-value >=0.3 (remaining=5275)
[2026-06-08T08:57:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5317)
[2026-06-08T08:57:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5260)
[2026-06-08T08:57:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5260)
[2026-06-08T08:57:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4701)
[2026-06-08T08:58:00] Searching for fusions with spliced split reads (remaining=4786)
[2026-06-08T08:58:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=3323)
[2026-06-08T08:58:06] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3287)
[2026-06-08T08:58:06] Searching for fusions with >=4 spliced events (remaining=3950)
[2026-06-08T08:58:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1744)
[2026-06-08T08:58:21] Filtering fusions with anchors <=23nt (remaining=1521)
[2026-06-08T08:58:21] Filtering end-to-end fusions with low support (remaining=1484)
[2026-06-08T08:58:22] Filtering fusions with no coverage around the breakpoints (remaining=1444)
[2026-06-08T08:58:22] Indexing gene sequences 
[2026-06-08T08:58:30] Filtering genes with >=30% identity (remaining=633)
[2026-06-08T08:58:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=425)
[2026-06-08T08:58:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=314)
[2026-06-08T08:58:42] Searching for additional isoforms (remaining=395)
[2026-06-08T08:58:44] Assigning confidence scores to events 
[2026-06-08T08:58:46] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:46] Writing fusions to file 'tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:58:49] Writing discarded fusions to file 'tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:16] Freeing resources
[2026-06-08T08:59:33] Done (elapsed time=00:12:53, CPU time=00:12:52, peak memory=15.2gb)