[2026-06-08T08:48:35] Launching Arriba 2.4.0
[2026-06-08T08:48:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:51] Reading chimeric alignments from 'tih_rna_sample_00570_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11506570)
[2026-06-08T08:56:27] Marking multi-mapping alignments (marked=6807815)
[2026-06-08T08:56:32] Detecting strandedness (reverse)
[2026-06-08T08:56:32] Assigning strands to alignments 
[2026-06-08T08:56:34] Annotating alignments 
[2026-06-08T08:57:14] Filtering duplicates (remaining=7195522)
[2026-06-08T08:57:23] 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=6974416)
[2026-06-08T08:57:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6974416)
[2026-06-08T08:57:28] Filtering viral contigs with expression lower than the top 5 (remaining=6974416)
[2026-06-08T08:57:34] Filtering viral contigs with less than 5% coverage (remaining=6974416)
[2026-06-08T08:57:36] Estimating fragment length (mate gap mean=-85.3673, mate gap stddev=27.6371, read length mean=128.78)
[2026-06-08T08:57:37] Filtering read-through fragments with a distance <=10000bp (remaining=6387989)
[2026-06-08T08:57:39] Filtering inconsistently clipped mates (remaining=6274829)
[2026-06-08T08:57:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6171393)
[2026-06-08T08:57:48] Filtering fragments with small insert size (remaining=6169738)
[2026-06-08T08:57:50] Filtering alignments with long gaps (remaining=6169737)
[2026-06-08T08:57:53] Filtering fragments with both mates in the same gene (remaining=6168763)
[2026-06-08T08:57:55] Filtering fusions arising from hairpin structures (remaining=5829534)
[2026-06-08T08:57:59] Filtering reads with a mismatch p-value <=0.01 (remaining=2851639)
[2026-06-08T08:58:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=1189247)
[2026-06-08T08:58:26] Finding fusions and counting supporting reads (total=895767)
[2026-06-08T08:58:46] Merging adjacent fusion breakpoints (remaining=884630)
[2026-06-08T08:58:48] Filtering multi-mapping fusions by alignment score and read support (remaining=580486)
[2026-06-08T08:59:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=579000)
[2026-06-08T08:59:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=275973)
[2026-06-08T08:59:39] Filtering fusions with <2 supporting reads (remaining=35858)
[2026-06-08T08:59:40] Filtering fusions with an e-value >=0.3 (remaining=7931)
[2026-06-08T08:59:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7996)
[2026-06-08T08:59:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7888)
[2026-06-08T08:59:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7888)
[2026-06-08T08:59:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7000)
[2026-06-08T08:59:54] Searching for fusions with spliced split reads (remaining=7118)
[2026-06-08T09:00:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=4431)
[2026-06-08T09:00:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4389)
[2026-06-08T09:00:02] Searching for fusions with >=4 spliced events (remaining=5497)
[2026-06-08T09:00:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2425)
[2026-06-08T09:00:18] Filtering fusions with anchors <=23nt (remaining=2055)
[2026-06-08T09:00:19] Filtering end-to-end fusions with low support (remaining=2021)
[2026-06-08T09:00:20] Filtering fusions with no coverage around the breakpoints (remaining=1980)
[2026-06-08T09:00:20] Indexing gene sequences 
[2026-06-08T09:00:27] Filtering genes with >=30% identity (remaining=527)
[2026-06-08T09:00:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=176)
[2026-06-08T09:00:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=163)
[2026-06-08T09:00:38] Searching for additional isoforms (remaining=204)
[2026-06-08T09:00:39] Assigning confidence scores to events 
[2026-06-08T09:00:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:43] Writing fusions to file 'tih_rna_sample_00570_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:45] Writing discarded fusions to file 'tih_rna_sample_00570_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:23] Freeing resources
[2026-06-08T09:01:46] Done (elapsed time=00:13:11, CPU time=00:13:11, peak memory=16gb)